35 research outputs found
Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT
Ferroplasmaceae represent ubiquitous iron-oxidising extreme acidophiles with a number of unique physiological traits. In a genome-based study of Ferroplasma acidiphilum YT, the only species of the genus Ferroplasma with a validly published name, we assessed its central metabolism and genome stability during a long-term cultivation experiment. Consistently with physiology, the genome analysis points to F. acidiphilum YT having an obligate peptidolytic oligotrophic lifestyle alongside with anaplerotic carbon assimilation. This narrow trophic specialisation abridges the sugar uptake, although all genes for glycolysis and gluconeogenesis, including bifunctional unidirectional fructose 1,6-bisphosphate aldolase/phosphatase, have been identified. Pyruvate and 2-oxoglutarate dehydrogenases are substituted by âancientâ CoA-dependent pyruvate and alpha-ketoglutarate ferredoxin oxidoreductases. In the lab culture, after ~550 generations, the strain exhibited the mutation rate of â„1.3âĂâ10â8 single nucleotide substitutions per site per generation, which is among the highest values recorded for unicellular organisms. All but one base substitutions were G:C to A:T, their distribution between coding and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the neutral drift being a prevalent mode in genome evolution in the lab culture. Mutations in nature seem to occur with lower frequencies, as suggested by a remarkable genomic conservation in F. acidiphilum YT variants from geographically distant populations
Metabarcoding of the kombucha microbial community grown in different microenvironments
Introducing of the DNA metabarcoding analysis of probiotic microbial communities allowed getting insight into their
functioning and establishing a better control on safety and efficacy of the probiotic communities. In this work the
kombucha poly-microbial probiotic community was analysed to study its flexibility under different growth conditions.
Environmental DNA sequencing revealed a complex and flexible composition of the kombucha microbial culture
(KMC) constituting more bacterial and fungal organisms in addition to those found by cultural method. The community
comprised bacterial and yeast components including cultured and uncultivable microorganisms. Culturing the
KMC under different conditions revealed the core part of the community which included acetobacteria of two genera
Komagataeibacter (former Gluconacetobacter) and Gluconobacter, and representatives of several yeast genera among
which Brettanomyces/Dekkera and Pichia (including former Issatchenkia) were dominant. Herbaspirillum spp. and Halomonas
spp., which previously had not been described in KMC, were found to be minor but permanent members of
the community. The community composition was dependent on the growth conditions. The bacterial component of
KMC was relatively stable, but may include additional memberâlactobacilli. The yeast species composition was significantly
variable. High-throughput sequencing showed complexity and variability of KMC that may affect the quality
of the probiotic drink. It was hypothesized that the kombucha core community might recruit some environmental
bacteria, particularly lactobacilli, which potentially may contribute to the fermentative capacity of the probiotic drink.
As many KMC-associated microorganisms cannot be cultured out of the community, a robust control for community
composition should be provided by using DNA metabarcoding.National Academy of Sciences of Ukraine (N47/2013)http://www.amb-express.comhb201
Metagenome-assembled genome sequences obtained from a reactivated kombucha microbial community exposed to a Mars-like environment outside the International Space Station
Kombucha is a traditional tea fermented by symbiotic microbiota, and it
has been known as a functional fermented product. Here, we report four microbial
metagenome-assembled genome sequences (MAGs) reconstructed from the microbiomes
in kombucha exposed to a Mars-like environment outside the International Space Station.The Bio & Medical Technology Development Program of the National Research Foundation of Korea (NRF), funded by the South Korean government (MSIT), and the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare.https://mra.asm.orgam2022BiochemistryGeneticsMicrobiology and Plant Patholog
Genomic analysis of Caldithrix abyssi, the thermophilic anaerobic bacterium of the novel bacterial phylum Calditrichaeota
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase ΔHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. OS and MSG were supported by the Russian Science Foundation (RSF, grant 14-24-00155). EB-O and SG were supported by the RSF grant 14-24-00165. IK, NC, AL, and MM were supported by the Russian Foundation for Basic Research grant 14-04-00503.http://www.frontiersin.orgam2017Biochemistr
Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp rimicaris exoculata by using functional metagenomics
The shrimp Rimicaris exoculata dominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth,
2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting
the R. exoculata gill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to
moderate identity to known esterase sequences (<52%) and to each other (11.9 to 63.7%) and appear to have originated from
unknown species or from genera of Proteobacteria related to Thiothrix/Leucothrix (MGS-RG1/RG2) and to the Rhodobacteraceae
group (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity
profiles of these enzymes. All 3 of these enzymes had greater esterase than lipase activity and exhibited specific activities with
ester substrates (<356Umg 1) in the range of similar enzymes. MGS-RG3 was inhibited by salts and pressure and had a low
optimal temperature (30°C), and its substrate profile clustered within a group of low-activity and substrate-restricted marine
enzymes. In contrast, MGS-RG1 and MGS-RG2 were most active at 45 to 50°C and were salt activated and barotolerant. They
also exhibited wider substrate profiles that were close to those of highly active promiscuous enzymes from a marine hydrothermal
vent (MGS-RG2) and from a cold brackish lake (MGS-RG1). The data presented are discussed in the context of promoting
the examination of enzyme activities of taxa found in habitats that have been neglected for enzyme prospecting; the enzymes
found in these taxa may reflect distinct habitat-specific adaptations and may constitute new sources of rare reaction specificities.The European
Community project MAMBA (FP7-KBBE-2008-226977), grant BIO2011-25012 from the Spanish Ministry of the
Economy and Competitiveness (formerly MICINN). P.N.G. and O.V.G.
were supported by EU FP7 project MICROB3 (FP7-OCEAN.2011
287589). This work received support from the Government of Canada
through Genome Canada and the Ontario Genomics Institute (grant
2009-OGI-ABC-1405 to A.F.Y. and A.S.) and from the U.S. National Institutes
of Health (grants GM074942 and GM094585 to A.S. through the
Midwest Center for Structural Genomics).http://aem.asm.orgam201
Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats
The present study provides a deeper view of protein
functionality as a function of temperature, salt and
pressure in deep-sea habitats. A set of eight different
enzymes from five distinct deep-sea (3040â4908 m
depth), moderately warm (14.0â16.5°C) biotopes,
characterized by a wide range of salinities (39â348
practical salinity units), were investigated for this
purpose. An enzyme from a âsuperficialâ marine
hydrothermal habitat (65°C) was isolated and characterized
for comparative purposes. We report here the
first experimental evidence suggesting that in saltsaturated
deep-sea habitats, the adaptation to high
pressure is linked to high thermal resistance (P
value = 0.0036). Salinity might therefore increase the
temperature window for enzyme activity, and possibly
microbial growth, in deep-sea habitats. As an
example, Lake Medee, the largest hypersaline deepsea
anoxic lake of the Eastern Mediterranean Sea,
where the water temperature is never higher than
16°C, was shown to contain halopiezophilic-like
enzymes that are most active at 70°C and with denaturing
temperatures of 71.4°C. The determination of
the crystal structures of five proteins revealed
unknown molecular mechanisms involved in protein
adaptation to poly-extremes as well as distinct active
site architectures and substrate preferences relative
to other structurally characterized enzymes.European Community project MAMBA (FP7-KBBE-2008-226977). This grant BIO2011-25012 from the Spanish Ministry of Economy and Competitiveness (formerly MICINN). European Commission for âMicroB3â grant (FP7-OCEAN.2011-2 (contract Nr
287589)). Government of Canada through Genome Canada
and the Ontario Genomics Institute (grant 2009-OGI-ABC-1405) and
U.S. National Institutes of Health (grants GM074942 and GM094585). Midwest Center for Structural Genomics).http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1462-2920hb2016Biochemistr
Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica
M.K. and P.N.G. designed the work; T.N.C. performed physiological studies; M.K., M.F.,
Y.A.-R., A.B., N.L.-C., M.E.G., O.R.K., T.Y.N., S.K., I.L., O.V.G., M.M.Y. R.R. and P.N.G.
were associated with genome annotation; H.J.H. performed lipids and FAME analysis;
M.F., M-l.F., S.J., S.C. and J.P.A performed chaperonin anti-proteome analysis; A.-x. S.,
O.K., O.E., P.A.P., P.S. and Y.K. were associated with structural proteomics; A.T. and R.F.
were associated with functional proteomics; H.L. performed electron microscopy; R.D.
performed real-time PCR; M.M.-G. and M.F. performed DIGE proteome analysis;
M.G. was involved in siderophore production; O.N.R. performed genomic islandsâ
analysis; H.T. performed storage lipid compoundsâ analysis; P.N.G. coordinated
manuscript writing.Accession Codes: The genome sequence of Oleispira antarctica RB-8 has been deposited
in GenBank under accession core FO203512. Protein structures have deposited in PDB
under accession codes 3QVM (a/b hydrolase, OLEAN_C08020), 3QVQ (phosphodiesterase,
OLEAN_C20330), 3M16 (transaldolase, OLEAN_C18160), 3LQY (isochorismatase,
OLEAN_C07660), 3LNP (amidohydrolase, OLEAN_C13880), 3V77/3L53 (fumarylacetoacetate isomerase/hydrolase, OLEAN_C35840), 3VCR/3LAB
(2-keto-3-deoxy-6-phosphogluconate aldolase, OLEAN_C25130), 3IRU (phoshonoacetaldehyde
hydrolase, OLEAN_C33610), 3I4Q (inorganic pyrophosphatase,
OLEAN_C30460), 3LMB (protein with unknown function, OLEAN_C10530).Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment
on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica
and show that compared with Alcanivorax borkumensisâthe paradigm of mesophilic
hydrocarbonoclastic bacteriaâO. antarctica has a larger genome that has witnessed massive
gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants,
siderophores and micronutrient-scavenging pathways. We also show that at low temperatures,
the main protein-folding machine Cpn60 functions as a single heptameric barrel that
uses larger proteins as substrates compared with the classical double-barrel structure
observed at higher temperatures. With 11 protein crystal structures, we further report the
largest set of structures from one psychrotolerant organism. The most common structural
feature is an increased content of surface-exposed negatively charged residues compared to
their mesophilic counterparts. Our findings are relevant in the context of microbial
cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold
environments.We acknowledge the funding from the EU Framework Program 7 to support Projects
MAMBA (226977), ULIXES (266473), MAGIC PAH (245226) and MICROB3 (287589)
This work received the support of the Government of Canada through Genome Canada
and the Ontario Genomics Institute (grant 2009-OGI-ABC-1405 to A.F.Y. and A.S.), and
the U.S. Government National Institutes of Health (grants GM074942 and GM094585
(to A.S. through Midwest Center for Structural Genomics). The study was supported by
the Max Planck Society and the Deutsche Forschungsgemeinschaft through project KU
2679/2-1 and BU 890/21-1. We thank the sequencing team of the AG Reinhardt for
technical assistance and Alfred Beck for computational support. The skilful work of
electron microscopic sample preparation by Mrs. Ingeborg Kristen (Dept. VAM, HZI
Braunschweig) is gratefully acknowledged. Authors thank Professor Ken Timmis for his
critical reading the manuscript and useful comments.http://www.nature.com/naturecommunicationsam201
The FGGY carbohydrate kinase family : insights into the evolution of functional specificities
© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Computational Biology 7 (2011): e1002318, doi:10.1371/journal.pcbi.1002318.Function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. However, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. Here, using the FGGY carbohydrate kinase family as an example, we built a confidently annotated reference set (CARS) of proteins by propagating experimentally verified functional assignments to a limited number of homologous proteins that are supported by their genomic and functional contexts. Then, we analyzed, on both the phylogenetic and the molecular levels, the evolution of different functional specificities in this family. The results show that the different functions (substrate specificities) encoded by FGGY kinases have emerged only once in the evolutionary history following an apparently simple divergent evolutionary model. At the same time, on the molecular level, one isofunctional group (L-ribulokinase, AraB) evolved at least two independent solutions that employed distinct specificity-determining residues for the recognition of a same substrate (L-ribulose). Our analysis provides a detailed model of the evolution of the FGGY kinase family. It also shows that only combined molecular and phylogenetic approaches can help reconstruct a full picture of functional diversifications in such diverse families.This study was funded by NIH and DOE grants
26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 - Meeting Abstracts - Antwerp, Belgium. 15â20 July 2017
This work was produced as part of the activities of FAPESP Research,\ud
Disseminations and Innovation Center for Neuromathematics (grant\ud
2013/07699-0, S. Paulo Research Foundation). NLK is supported by a\ud
FAPESP postdoctoral fellowship (grant 2016/03855-5). ACR is partially\ud
supported by a CNPq fellowship (grant 306251/2014-0)
Shotgun metagenomic analysis of kombucha mutualistic community exposed to Marsâlike environment outside the International Space Station
Kombucha is a multispecies microbial ecosystem mainly composed of acetic acid bacteria and osmophilic acidâtolerant yeasts, which is used to produce a probiotic drink. Furthermore, Kombucha Mutualistic Community (KMC) has been recently proposed to be used during long space missions as both a living functional fermented product to improve astronauts' health and an efficient source of bacterial nanocellulose. In this study, we compared KMC structure and functions before and after samples were exposed to the space/Marsâlike environment outside the International Space Station in order to investigate the changes related to their reâadaptation to Earthâlike conditions by shotgun metagenomics, using both diversity and functional analyses of Community Ecology and Complex Networks approach. Our study revealed that the longâterm exposure to space/Marsâlike conditions on low Earth orbit may disorganize the KMC to such extent that it will not restore the initial community structure; however, KMC core microorganisms of the community were maintained. Nonetheless, there were no significant differences in the community functions, meaning that the KMC communities are ecologically resilient. Therefore, despite the extremely harsh conditions, key KMC species revived and provided the community with the genetic background needed to survive long periods of time under extraterrestrial conditions.Figure S1. Stacked bar charts presenting the bacterial (A, B), yeast (C, D), and viral (E, F) components of postflight kombucha microbial communities (KMCâb) and corresponding KMCs cultured within 2.5 year (KMC_c). (1: top, UVâunprotected level; 2: middle, UVâprotected level; 3: bottom, UVâprotected level, 4: laboratoryâkept KMC samples during the exposure experiment; 5: the initial KMC sample). Dark and light blue colour for references (KMC_5 and KMC_4 respectively). The space exposed samples are represented in gradient colour of brown for yeasts, and green for viruses.Figure S2. Relative abundance of the dominant bacterial genera (A) Komagataeibacter and (B) Gluconobacter.Table S1. Alphaâdiversity parameters estimated for the experimental and control KMCs.SERBâEMEQ/051/2014, EEQ/2018/001085, UGCâNFHEST fellowship Government of India, the National Academy of Sciences of Ukraine, the Graduate Programs of Microbiology and Bioinformatics of the Universidade Federal de Minas Gerais (UFMG), and CNPq (Brazil) for the scientific productivity scholarships.https://sfamjournals.onlinelibrary.wiley.com/journal/146229202022-01-21hj2021BiochemistryGeneticsMicrobiology and Plant Patholog