Reconstructing Genomes of Carbon Monoxide Oxidisers in Volcanic Deposits Including Members of the Class Ktedonobacteria

Microorganisms can potentially colonise volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H2) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of 380, 269 and 63 years, respectively. A total of 19 metagenome-assembled genomes (MAGs) were retrieved from all stages with a higher number observed in the youngest soil (1640: 2 MAGs, 1751: 1 MAG, 1957: 16 MAGs). Genomic similarity indices showed that several MAGs had amino-acid identity (AAI) values >50% to the phyla Actinobacteria, Acidobacteria, Gemmatimonadetes, Proteobacteria and Chloroflexi. Three MAGs from the youngest site (1957) belonged to the class Ktedonobacteria (Chloroflexi). Complete cellular functions of all the MAGs were characterised, including carbon fixation, terpenoid backbone biosynthesis, formate oxidation and CO oxidation. All 19 environmental genomes contained at least one gene encoding a putative carbon monoxide dehydrogenase (CODH). Three MAGs had form I coxL operon (encoding the large subunit CO-dehydrogenase). One of these MAGs (MAG-1957-2.1, Ktedonobacterales) was highly abundant in the youngest soil. MAG-1957-2.1 also contained genes encoding a [NiFe]-hydrogenase and hyp genes encoding accessory enzymes and proteins. Little is known about the Ktedonobacterales through cultivated isolates, but some species can utilise H2 and CO for growth. Our results strongly suggest that the remote volcanic sites in Chile represent a natural habitat for Ktedonobacteria and they may use reduced gases for growth.

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Reconstructing genomes of carbon monoxide oxidisers in volcanic deposits including members of the class Ktedonobacteria

10.1101/2020.10.29.361295 ◽

2020 ◽

Author(s):

Marcela Hernández ◽

Blanca Vera-Gargallo ◽

Marcela Calabi-Floody ◽

Gary M King ◽

Ralf Conrad ◽

...

Keyword(s):

Carbon Monoxide ◽

Carbon Fixation ◽

Large Subunit ◽

Natural Habitat ◽

Volcanic Rocks ◽

Amino Acid Identity ◽

Cellular Functions ◽

Gene Encoding ◽

Genes Encoding ◽

Successional Stages

AbstractMicroorganisms can potentially colonize volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H2) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of 380, 269 and 63 years, respectively. A total of 19 metagenome-assembled genomes (MAGs) were retrieved from all stages with a higher number observed in the youngest soil (1640: 2 MAGs, 1751: 1 MAG, 1957: 16 MAGs). Genomic similarity indices showed that several MAGs had amino-acid identity (AAI) values >50% to the phyla Actinobacteria, Acidobacteria, Gemmatimonadetes, Proteobacteria and Chloroflexi. Three MAGs from the youngest site (1957) belonged to the class Ktedonobacteria (Chloroflexi). Complete cellular functions of all the MAGs were characterised, including carbon fixation, terpenoid backbone biosynthesis, formate oxidation and CO oxidation. All 19 environmental genomes contained at least one gene encoding a putative carbon monoxide dehydrogenase (CODH). Three MAGs had form I coxL operon (encoding the large subunit CO-dehydrogenase). One of these MAGs (MAG-1957-2.1, Ktedonobacterales) was highly abundant in the youngest soil. MAG-1957-2.1 also contained genes encoding a [NiFe]-hydrogenase and hyp genes encoding accessory enzymes and proteins. Little is known about the Ktedonobacterales through cultivated isolates, but some species can utilize H2 and CO for growth. Our results strongly suggest that the remote volcanic sites in Chile represent a natural habitat for Ktedonobacteria and they may use reduced gases for growth.

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Occurrence, phylogeny and evolution of ribulose-1,5-bisphosphate carboxylase/oxygenase genes in obligately chemolithoautotrophic sulfur-oxidizing bacteria of the genera Thiomicrospira and Thioalkalimicrobium

Microbiology ◽

10.1099/mic.0.28699-0 ◽

2006 ◽

Vol 152 (7) ◽

pp. 2159-2169 ◽

Cited By ~ 27

Author(s):

Tatjana P. Tourova ◽

Elizaveta M. Spiridonova ◽

Ivan A. Berg ◽

Boris B. Kuznetsov ◽

Dimitry Yu. Sorokin

Keyword(s):

16S Rrna ◽

Large Subunit ◽

Gene Encoding ◽

Bisphosphate Carboxylase ◽

Phylogenetic Cluster ◽

New Family ◽

Genes Encoding ◽

Key Enzyme ◽

Sulfur Oxidizing ◽

Phylogeny And Evolution

The occurrence of the different genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the key enzyme of the Calvin–Benson–Bassham cycle of autotrophic CO2 fixation, was investigated in the members of the genus Thiomicrospira and the relative genus Thioalkalimicrobium, all obligately chemolithoautotrophic sulfur-oxidizing Gammaproteobacteria. The cbbL gene encoding the ‘green-like’ form I RubisCO large subunit was found in all analysed species, while the cbbM gene encoding form II RubisCO was present only in Thiomicrospira species. Furthermore, species belonging to the Thiomicrospira crunogena 16S rRNA-based phylogenetic cluster also possessed two genes of green-like form I RubisCO, cbbL-1 and cbbL-2. Both 16S-rRNA- and cbbL-based phylogenies of the Thiomicrospira–Thioalkalimicrobium–Hydrogenovibrio group were congruent, thus supporting its monophyletic origin. On the other hand, it also supports the necessity for taxonomy reorganization of this group into a new family with four genera.

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The carB Gene Encoding the Large Subunit of Carbamoylphosphate Synthetase from Lactococcus lactis Is Transcribed Monocistronically

Journal of Bacteriology ◽

10.1128/jb.180.17.4380-4386.1998 ◽

1998 ◽

Vol 180 (17) ◽

pp. 4380-4386 ◽

Cited By ~ 27

Author(s):

Jan Martinussen ◽

Karin Hammer

Keyword(s):

Lactococcus Lactis ◽

Large Subunit ◽

Arginine Deiminase ◽

Gene Encoding ◽

Pyrimidine Nucleotides ◽

Reading Frame ◽

Glutathione Peroxidases ◽

Carbamoylphosphate Synthetase ◽

Genes Encoding ◽

High Degree

ABSTRACT The biosynthesis of carbamoylphosphate is catalyzed by the heterodimeric enzyme carbamoylphosphate synthetase. The genes encoding the two subunits of this enzyme in procaryotes are normally transcribed as an operon, but the gene encoding the large subunit (carB) in Lactococcus lactis is shown to be transcribed as an isolated unit. Carbamoylphosphate is a precursor in the biosynthesis of both pyrimidine nucleotides and arginine. By mutant analysis,L. lactis is shown to possess only onecarB gene; the same gene product is thus required for both biosynthetic pathways. Furthermore, arginine may satisfy the requirement for carbamoylphosphate in pyrimidine biosynthesis through degradation by means of the arginine deiminase pathway. The expression of the carB gene is subject to regulation at the level of transcription by pyrimidines, most probably by an attenuator mechanism. Upstream of the carB gene, an open reading frame showing a high degree of similarity to those of glutathione peroxidases from other organisms was identified.

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Molecular and Immunological Analyses of the Mycobacterium avium Homolog of the Immunodominant Mycobacterium leprae 35-Kilodalton Protein

Infection and Immunity ◽

10.1128/iai.66.6.2684-2690.1998 ◽

1998 ◽

Vol 66 (6) ◽

pp. 2684-2690 ◽

Cited By ~ 22

Author(s):

James A. Triccas ◽

Nathalie Winter ◽

Paul W. Roche ◽

Andrea Gilpin ◽

Kathleen E. Kendrick ◽

...

Keyword(s):

Amino Acid ◽

Mycobacterium Avium ◽

Amino Acid Level ◽

Streptomyces Griseus ◽

Amino Acid Identity ◽

Delayed Type Hypersensitivity ◽

Gene Encoding ◽

Genes Encoding ◽

Species Specific ◽

35 Kda Protein

ABSTRACT The analysis of host immunity to mycobacteria and the development of discriminatory diagnostic reagents relies on the characterization of conserved and species-specific mycobacterial antigens. In this report, we have characterized the Mycobacterium avium homolog of the highly immunogenic M. leprae 35-kDa protein. The genes encoding these two proteins were well conserved, having 82% DNA identity and 90% identity at the amino acid level. Moreover both proteins, purified from the fast-growing host M. smegmatis, formed multimeric complexes of around 1000 kDa in size and were antigenically related as assessed through their recognition by antibodies and T cells from M. leprae-infected individuals. The 35-kDa protein exhibited significant sequence identity with proteins from Streptomyces griseus and the cyanobacterium Synechoccocus sp. strain PCC 7942 that are up-regulated under conditions of nutrient deprivation. The 67% amino acid identity between the M. avium 35-kDa protein and SrpI of Synechoccocus was spread across the sequences of both proteins, while the homologous regions of the 35-kDa protein and the P3 sporulation protein of S. griseus were interrupted in the P3 protein by a divergent central region. Assessment by PCR demonstrated that the gene encoding the M. avium35-kDa protein was present in all 30 M. avium clinical isolates tested but absent from M. intracellulare,M. tuberculosis, or M. bovis BCG. Mice infected with M. avium, but not M. bovis BCG, developed specific immunoglobulin G antibodies to the 35-kDa protein, consistent with the observation that tuberculosis patients do not recognize the antigen. Strong delayed-type hypersensitivity was elicited by the protein in guinea pigs sensitized with M. avium.

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Aerobic carboxydotrophy under extremely haloalkaline conditions in Alkalispirillum/Alkalilimnicola strains isolated from soda lakes

Microbiology ◽

10.1099/mic.0.033712-0 ◽

2010 ◽

Vol 156 (3) ◽

pp. 819-827 ◽

Cited By ~ 19

Author(s):

Dimitry Yu. Sorokin ◽

Tatjana P. Tourova ◽

Olga L. Kovaleva ◽

J. Gijs Kuenen ◽

Gerard Muyzer

Keyword(s):

Carbon Fixation ◽

Soda Lakes ◽

Large Subunit ◽

Calvin Cycle ◽

Soda Lake ◽

Protein Profiling ◽

Bacterial Strains ◽

Gene Encoding ◽

Respiration Activity ◽

Ph Range

Aerobic enrichments from soda lake sediments with CO as the only substrate resulted in the isolation of five bacterial strains capable of autotrophic growth with CO at extremely high pH and salinity. The strains belonged to the Alkalispirillum/Alkalilimnicola cluster in the Gammaproteobacteria, where the ability to oxidize CO, but not growth with CO, has been demonstrated previously. The growth with CO was possible only at an oxygen concentration below 5 % and CO concentration below 20 % in the gas phase. The isolates were also capable of growth with formate but not with H2. The carboxydotrophic growth occurred within a narrow pH range from 8 to 10.5 (optimum at 9.5) and a broad salt concentration from0.3 to 3.5 M total Na+ (optimum at 1.0 M). Cells grown on CO had high respiration activity with CO and formate, while the cells grown on formate actively oxidized formate alone. In CO-grown cells, CO-dehydrogenase (CODH) activity was detectable both in soluble and membrane fractions, while the NAD-independent formate dehydrogenase (FDH) resided solely in membranes. The results of total protein profiling and the failure to detect CODH with conventional primers for the coxL gene indicated that the CO-oxidizing enzyme in haloalkaliphilic isolates might differ from the classical aerobic CODH complex. A single cbbL gene encoding the RuBisCO large subunit was detected in all strains, suggesting the presence of the Calvin cycle of inorganic carbon fixation. Overall, these results demonstrated the possibility of aerobic carboxydotrophy under extremely haloalkaline conditions.

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Cloning, expression, and characterization of Baeyer–Villiger monooxygenases from eukaryotic Exophiala jeanselmei strain KUFI-6N

Bioscience Biotechnology and Biochemistry ◽

10.1093/bbb/zbab079 ◽

2021 ◽

Author(s):

Taisei Yamamoto ◽

Kento Kobayashi ◽

Yoshie Hasegawa ◽

Hiroaki Iwaki

Keyword(s):

Escherichia Coli ◽

Catalytic Efficiency ◽

Amino Acid Identity ◽

Membered Ring ◽

Gene Encoding ◽

Exophiala Jeanselmei ◽

Genes Encoding ◽

Substrate Spectrum ◽

Villiger Oxidation

Abstract The fungus Exophiala jeanselmei strain KUFI-6N produces a unique cycloalkanone monooxygenase (ExCAMO) that displays an uncommon substrate spectrum of Baeyer–Villiger oxidation of 4–10-membered ring ketones. In this study, we aimed to identify and sequence the gene encoding ExCAMO from KUFI-6N and overexpress the gene in Escherichia coli. We found that the primary structure of ExCAMO is most closely related to the cycloalkanone monooxygenase from Cylindrocarpon radicicola ATCC 11011, with 54.2% amino acid identity. ExCAMO was functionally expressed in Escherichia coli and its substrate spectrum and kinetic parameters investigated. Substrate profiling indicated that ExCAMO is unusual among known Baeyer–Villiger monooxygenases owing to its ability to accept a variety of substrates, including C4–C12 membered ring ketones. ExCAMO has high affinity and catalytic efficiency toward cycloalkanones, the highest being toward cyclohexanone. Five other genes encoding Baeyer–Villiger monooxygenases were also cloned and expressed in Escherichia coli.

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Expression and function of the cdgD gene, encoding a CHASE–PAS-DGC-EAL domain protein, in Azospirillum brasilense

Scientific Reports ◽

10.1038/s41598-020-80125-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

José Francisco Cruz-Pérez ◽

Roxana Lara-Oueilhe ◽

Cynthia Marcos-Jiménez ◽

Ricardo Cuatlayotl-Olarte ◽

María Luisa Xiqui-Vázquez ◽

...

Keyword(s):

Azospirillum Brasilense ◽

Type Strain ◽

Wild Type Strain ◽

Soil Conditions ◽

Wild Type ◽

Gene Encoding ◽

Wheat Roots ◽

Genes Encoding ◽

In The Wild ◽

Plant Growth Promoting

AbstractThe plant growth-promoting bacterium Azospirillum brasilense contains several genes encoding proteins involved in the biosynthesis and degradation of the second messenger cyclic-di-GMP, which may control key bacterial functions, such as biofilm formation and motility. Here, we analysed the function and expression of the cdgD gene, encoding a multidomain protein that includes GGDEF-EAL domains and CHASE and PAS domains. An insertional cdgD gene mutant was constructed, and analysis of biofilm and extracellular polymeric substance production, as well as the motility phenotype indicated that cdgD encoded a functional diguanylate protein. These results were correlated with a reduced overall cellular concentration of cyclic-di-GMP in the mutant over 48 h compared with that observed in the wild-type strain, which was recovered in the complemented strain. In addition, cdgD gene expression was measured in cells growing under planktonic or biofilm conditions, and differential expression was observed when KNO3 or NH4Cl was added to the minimal medium as a nitrogen source. The transcriptional fusion of the cdgD promoter with the gene encoding the autofluorescent mCherry protein indicated that the cdgD gene was expressed both under abiotic conditions and in association with wheat roots. Reduced colonization of wheat roots was observed for the mutant compared with the wild-type strain grown in the same soil conditions. The Azospirillum-plant association begins with the motility of the bacterium towards the plant rhizosphere followed by the adsorption and adherence of these bacteria to plant roots. Therefore, it is important to study the genes that contribute to this initial interaction of the bacterium with its host plant.

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Structure, expression, chromosomal location and product of the gene encoding Adh2 in Petunia.

Genetics ◽

10.1093/genetics/133.4.999 ◽

1993 ◽

Vol 133 (4) ◽

pp. 999-1007

Author(s):

R G Gregerson ◽

L Cameron ◽

M McLean ◽

P Dennis ◽

J Strommer

Keyword(s):

Chromosomal Location ◽

Higher Plants ◽

Gene Encoding ◽

Genomic Libraries ◽

Regulatory Strategy ◽

Adh1 Gene ◽

Adh Genes ◽

Genes Encoding ◽

Adh Gene ◽

Polymerase Chain

Abstract In most higher plants the genes encoding alcohol dehydrogenase comprise a small gene family, usually with two members. The Adh1 gene of Petunia has been cloned and analyzed, but a second identifiable gene was not recovered from any of three genomic libraries. We have therefore employed the polymerase chain reaction to obtain the major portion of a second Adh gene. From sequence, mapping and northern data we conclude this gene encodes ADH2, the major anaerobically inducible Adh gene of Petunia. The availability of both Adh1 and Adh2 from Petunia has permitted us to compare their structures and patterns of expression to those of the well-studied Adh genes of maize, of which one is highly expressed developmentally, while both are induced in response to hypoxia. Despite their evolutionary distance, evidenced by deduced amino acid sequence as well as taxonomic classification, the pairs of genes are regulated in strikingly similar ways in maize and Petunia. Our findings suggest a significant biological basis for the regulatory strategy employed by these distant species for differential expression of multiple Adh genes.

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Non-Syndromic Dentinogenesis Imperfecta Caused by Mild Mutations in COL1A2

Journal of Personalized Medicine ◽

10.3390/jpm11060526 ◽

2021 ◽

Vol 11 (6) ◽

pp. 526

Author(s):

Yejin Lee ◽

Youn Jung Kim ◽

Hong-Keun Hyun ◽

Jae-Cheoun Lee ◽

Zang Hee Lee ◽

...

Keyword(s):

Collagen Type ◽

Molecular Genetic ◽

Collagen Type I ◽

Type I ◽

Dentinogenesis Imperfecta ◽

Gene Encoding ◽

Korean Families ◽

Whole Exome ◽

Genes Encoding ◽

Candidate Gene Sequencing

Hereditary dentin defects can be categorized as a syndromic form predominantly related to osteogenesis imperfecta (OI) or isolated forms without other non-oral phenotypes. Mutations in the gene encoding dentin sialophosphoprotein (DSPP) have been identified to cause dentinogenesis imperfecta (DGI) Types II and III and dentin dysplasia (DD) Type II. While DGI Type I is an OI-related syndromic phenotype caused mostly by monoallelic mutations in the genes encoding collagen type I alpha 1 chain (COL1A1) and collagen type I alpha 2 chain (COL1A2). In this study, we recruited families with non-syndromic dentin defects and performed candidate gene sequencing for DSPP exons and exon/intron boundaries. Three unrelated Korean families were further analyzed by whole-exome sequencing due to the lack of the DSPP mutation, and heterozygous COL1A2 mutations were identified: c.3233G>A, p.(Gly1078Asp) in Family 1 and c.1171G>A, p.(Gly391Ser) in Family 2 and 3. Haplotype analysis revealed different disease alleles in Families 2 and 3, suggesting a mutational hotspot. We suggest expanding the molecular genetic etiology to include COL1A2 for isolated dentin defects in addition to DSPP.

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