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Zhou J, Feng Y, Wu X, Feng Y, Zhao Y, Pan J, Liu S. Communication leads to bacterial heterogeneous adaptation to changing conditions in partial nitrification reactor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172110. [PMID: 38565348 DOI: 10.1016/j.scitotenv.2024.172110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024]
Abstract
Recently, it is reported that bacterial communication coordinates the whole consortia to jointly resist the adverse environments. Here, we found the bacterial communication inevitably distinguished bacterial adaptation among different species in partial nitrification reactor under decreasing temperatures. We operated a partial nitrification reactor under temperature gradient from 30 °C to 5 °C and found the promotion of bacterial communication on adaptation of ammonia-oxidizing bacteria (AOB) was greater than that of nitrite-oxidizing bacteria (NOB). Signal pathways with single-component sensing protein in AOB can regulate more genes involved in bacterial adaptation than that with two-component sensing protein in NOB. The negative effects of bacterial communication, which were seriously ignored, have been highlighted, and Clp regulator downstream diffusible signal factor (DSF) based signal pathways worked as transcription activators and inhibitors of adaptation genes in AOB and NOB respectively. Bacterial communication can induce differential adaptation through influencing bacterial interactions. AOB inclined to cooperate with DSF synthesis bacteria as temperature declined, however, cooperation between NOB and DSF synthesis bacteria inclined to get weakening. According to the regulatory effects of signal pathways, bacterial survival strategies for self-protection were revealed. This study hints a potential way to govern niche differentiation in the microbiota by bacterial communication, contributing to forming an efficient artificial ecosystem.
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Affiliation(s)
- Jianhang Zhou
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Ying Feng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Xiaogang Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yiming Feng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yunpeng Zhao
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Juejun Pan
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Sitong Liu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China.
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Giovannini M, Vieri W, Bosi E, Riccardi C, Lo Giudice A, Fani R, Fondi M, Perrin E. Functional Genomics of a Collection of Gammaproteobacteria Isolated from Antarctica. Mar Drugs 2024; 22:238. [PMID: 38921549 PMCID: PMC11205219 DOI: 10.3390/md22060238] [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: 04/22/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, and Psychrobacter. Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.
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Affiliation(s)
- Michele Giovannini
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Walter Vieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Emanuele Bosi
- Department of Earth, Environment and Life Sciences—DISTAV, University of Genoa, Corso Europa 26, I-16132 Genova, Italy;
| | - Christopher Riccardi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA 90089, USA
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council, (CNR.ISP), Spianata San Raineri 86, I-98122 Messina, Italy;
- Italian Collection of Antarctic Bacteria, National Antarctic Museum (CIBAN-MNA), I-98122 Messina, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, I-90133 Palermo, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
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3
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Kastner PD, Noell SE, Essig DA. Complete genome sequence of a winter season Vibrio facilitates discovery of a novel subclade of cold-adapted species in the albus clade. Microb Genom 2024; 10:001178. [PMID: 38230915 PMCID: PMC10868602 DOI: 10.1099/mgen.0.001178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024] Open
Abstract
In temperate marine climate zones, seasonal changes in water temperature contribute to distinct populations of warm- and cold-water vibrios. We report here the complete genome sequence (BUSCO score=94.8) of the novel strain Vibrio sp. VB16 isolated in late winter from the intertidal zone near Virginia Beach, Virginia, USA with the ability to form colonies at 4 °C. The 5.2 Mbp genome is composed of a large (3.6 Mbp) and small (1.6 Mbp) chromosome. Based on paired average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH), V. sp. VB16 is the same species as V. sp. UBA2437 from a North Sea tidal flat and is closely related to V. sp. DW001 from Antarctic sea ice. Our phylogenomic and bioinformatic analyses placed VB16, UBA2437 and DW001 into a cold-tolerant subclade within the albus clade, along with two non-cold-tolerant subclades. Orthovenn analysis indicated that VB16 and its other albus clade members shared 1544 gene orthologue clusters, including clusters for biosynthesis of polar flagella and tight adhesion pili that predict multiple lifestyles, either free-living or as an opportunistic pathogen within a marine eukaryotic host. The cold-tolerant subclade shared 552 orthologue proteins, including genes known to promote survival in cold or freezing temperatures, such as the eicosapentaenoic acid biosynthetic gene cluster, syp exopolysaccharide gene cluster and novel giant proteins with ice-binding domains. This subclade represents a group of psychrotolerant or 'moderate psychrophile' winter season Vibrio species. The discovery of this subclade opens the door for experimental work on the physiological features, virulence potential and ecological importance of this subclade.
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Affiliation(s)
- Paul D. Kastner
- School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Stephen E. Noell
- Te Aka Mātuatua – School of Science, Thermophile Research Unit, Te Whare Wānanga o Waikato – University of Waikato, Hamilton, New Zealand
| | - David A. Essig
- Department of Biology, Geneva College, Beaver Falls, PA, USA
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4
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de Francisco Martínez P, Morgante V, González-Pastor JE. Isolation of novel cold-tolerance genes from rhizosphere microorganisms of Antarctic plants by functional metagenomics. Front Microbiol 2022; 13:1026463. [DOI: 10.3389/fmicb.2022.1026463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
The microorganisms that thrive in Antarctica, one of the coldest environments on the planet, have developed diverse adaptation mechanisms to survive in these extreme conditions. Through functional metagenomics, in this work, 29 new genes related to cold tolerance have been isolated and characterized from metagenomic libraries of microorganisms from the rhizosphere of two Antarctic plants. Both libraries were hosted in two cold-sensitive strains of Escherichia coli: DH10B ΔcsdA and DH10B ΔcsdA Δrnr. The csdA gene encodes a DEAD-box RNA helicase and rnr gene encodes an exoribonuclease, both essential for cold-adaptation. Cold-tolerance tests have been carried out in solid and liquid media at 15°C. Among the cold-tolerance genes identified, 12 encode hypothetical and unknown proteins, and 17 encode a wide variety of different proteins previously related to other well-characterized ones involved in metabolism reactions, transport and membrane processes, or genetic information processes. Most of them have been connected to cold-tolerance mechanisms. Interestingly, 13 genes had no homologs in E. coli, thus potentially providing entirely new adaptation strategies for this bacterium. Moreover, ten genes also conferred resistance to UV-B radiation, another extreme condition in Antarctica.
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Kouba V, Bachmannová C, Podzimek T, Lipovová P, van Loosdrecht MCM. Physiology of anammox adaptation to low temperatures and promising biomarkers: A review. BIORESOURCE TECHNOLOGY 2022; 349:126847. [PMID: 35167904 DOI: 10.1016/j.biortech.2022.126847] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The adaptation of bacteria involved in the anaerobic ammonium oxidation (anammox) to low temperatures in the mainstream of WWTP will unlock substantial treatment savings. However, their adaptation mechanisms have begun to be revealed only very recently. This study reviewed the state-of-the-art knowledge on these mechanisms from -omics studies, crucially including metaproteomics and metabolomics. Anammox bacteria adapt to low temperatures by synthesizing both chaperones of RNA and proteins and chemical chaperones. Furthermore, they preserve energy for the core metabolism by reducing biosynthesis in general. Thus, in this study, a number of biomarkers are proposed to help practitioners assess the extent of anammox bacteria adaptation and predict the decomposition of biofilms/granules or slower growth. The promising biomarkers also include unique ladderane lipids. Further proteomic and metabolomic studies are necessary for a more detailed understanding of anammox low-temperature adaptation, thus easing the transition to more cost-effective and sustainable wastewater treatment.
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Affiliation(s)
- V Kouba
- University of Chemistry and Technology Prague, Department of Water Technology and Environmental Engineering, Technická 5, 166 28 Prague, Czechia.
| | - Ch Bachmannová
- University of Chemistry and Technology Prague, Department of Water Technology and Environmental Engineering, Technická 5, 166 28 Prague, Czechia
| | - T Podzimek
- University of Chemistry and Technology Prague, Department of Biochemistry and Microbiology, Technická 5, 166 28 Prague, Czechia
| | - P Lipovová
- University of Chemistry and Technology Prague, Department of Biochemistry and Microbiology, Technická 5, 166 28 Prague, Czechia
| | - M C M van Loosdrecht
- The Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
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A meta-analysis of the activity, stability, and mutational characteristics of temperature-adapted enzymes. Biosci Rep 2021; 41:228416. [PMID: 33871022 PMCID: PMC8150157 DOI: 10.1042/bsr20210336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/29/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Understanding the characteristics that define temperature-adapted enzymes has been a major goal of extremophile enzymology in recent decades. In the present study, we explore these characteristics by comparing psychrophilic, mesophilic, and thermophilic enzymes. Through a meta-analysis of existing data, we show that psychrophilic enzymes exhibit a significantly larger gap (Tg) between their optimum and melting temperatures compared with mesophilic and thermophilic enzymes. These results suggest that Tg may be a useful indicator as to whether an enzyme is psychrophilic or not and that models of psychrophilic enzyme catalysis need to account for this gap. Additionally, by using predictive protein stability software, HoTMuSiC and PoPMuSiC, we show that the deleterious nature of amino acid substitutions to protein stability increases from psychrophiles to thermophiles. How this ultimately affects the mutational tolerance and evolutionary rate of temperature adapted organisms is currently unknown.
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7
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Cold survival strategies for bacteria, recent advancement and potential industrial applications. Arch Microbiol 2018; 201:1-16. [PMID: 30478730 DOI: 10.1007/s00203-018-1602-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/04/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022]
Abstract
Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.
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Ma W, Jia J, Huang X, Xie W, Zhang X, Tang J, Lin C, Zhao L, Fang P. Stable isotope labelling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Edwardsiella tarda ATCC 15947 under prolonged cold stress. Microb Pathog 2018; 125:12-19. [PMID: 30201590 DOI: 10.1016/j.micpath.2018.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 09/01/2018] [Accepted: 09/05/2018] [Indexed: 01/15/2023]
Abstract
Edwardsiella tarda poses a threat to human health and has resulted in enormous economic losses in aquaculture. Low temperatures are usually applied to contain the growth of this microorganism. In this study, stable isotope labelling by amino acids in cell culture (SILAC) was used to conduct comparative proteomic quantitation of E. tarda ATCC 15947 under cold stress for two weeks. We identified 1391 proteins, of which 898 were quantifiable. Of these, 72 proteins were upregulated and 164 were downregulated in response to cold stress. Even though E. tarda ATCC 15947 is not a psychrophile, several key proteins related to DNA synthesis and transcription were significantly upregulated. Additionally, proteins related to haemolytic activities and gluconeogenesis were upregulated, even though E. tarda ATCC 15497 is considered non-virulent in aquaculture. This study therefore delineated the specific proteomic response of this E. tarda ATCC 15947 to prolonged cold stress.
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Affiliation(s)
- Weixing Ma
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China; Qingdao University of Science and Technology, No. 53, Zhengzhou Road, Qingdao, 266042, China
| | - Juntao Jia
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China.
| | - Xiaohua Huang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Wancui Xie
- Qingdao University of Science and Technology, No. 53, Zhengzhou Road, Qingdao, 266042, China
| | - Xiaoliang Zhang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Jing Tang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Chao Lin
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Liqing Zhao
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
| | - Peipei Fang
- Shandong Entry-Exit Inspection and Quarantine Bureau, No. 70, Qutangxia Road, Qingdao, 266002, China
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9
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Polyunsaturated fatty acids in marine bacteria and strategies to enhance their production. Appl Microbiol Biotechnol 2018; 102:5811-5826. [PMID: 29749565 DOI: 10.1007/s00253-018-9063-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 10/16/2022]
Abstract
Polyunsaturated fatty acids (PUFAs) play an important role in human diet. Despite the wide-ranging importance and benefits from heart health to brain functions, humans and mammals cannot synthesize PUFAs de novo. The primary sources of PUFA are fish and plants. Due to the increasing concerns associated with food security as well as issues of environmental contaminants in fish oil, there has been considerable interest in the production of polyunsaturated fatty acids from alternative resources which are more sustainable, safer, and economical. For instance, marine bacteria, particularly the genus of Shewanella, Photobacterium, Colwellia, Moritella, Psychromonas, Vibrio, and Alteromonas, are found to be one among the major microbial producers of polyunsaturated fatty acids. Recent developments in the area with a focus on the production of polyunsaturated fatty acids from marine bacteria as well as the metabolic engineering strategies for the improvement of PUFA production are discussed.
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10
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Fiedoruk K, Drewnowska JM, Daniluk T, Leszczynska K, Iwaniuk P, Swiecicka I. Ribosomal background of the Bacillus cereus group thermotypes. Sci Rep 2017; 7:46430. [PMID: 28406161 PMCID: PMC5390287 DOI: 10.1038/srep46430] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/08/2017] [Indexed: 11/09/2022] Open
Abstract
In this study we reconstructed the architecture of Bacillus cereus sensu lato population based on ribosomal proteins, and identified a link between the ribosomal proteins’ variants and thermal groups (thermotypes) of the bacilli. The in silico phyloproteomic analysis of 55 ribosomal proteins (34 large and 21 small subunit r-proteins) of 421 strains, representing 14 well-established or plausible B. cereus sensu lato species, revealed several ribosomal clusters (r-clusters), which in general were well correlated with the strains’ affiliation to phylogenetic/thermal groups I–VII. However, a conformity and possibly a thermal characteristic of certain phylogenetic groups, e.g. the group IV, were not supported by a distribution of the corresponding r-clusters, and consequently neither by the analysis of cold-shock proteins (CSPs) nor by a content of heat shock proteins (HSPs). Furthermore, a preference for isoleucine and serine over valine and alanine in r-proteins along with a lack of HSP16.4 were recognized in non-mesophilic thermotypes. In conclusion, we suggest that the observed divergence in ribosomal proteins may be connected with an adaptation of B. cereus sensu lato members to various thermal niches.
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Affiliation(s)
- Krzysztof Fiedoruk
- Department of Microbiology, Medical University of Bialystok, Bialystok, Poland
| | - Justyna M Drewnowska
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland
| | - Tamara Daniluk
- Department of Microbiology, Medical University of Bialystok, Bialystok, Poland
| | | | - Piotr Iwaniuk
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland
| | - Izabela Swiecicka
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland.,Laboratory of Applied Microbiology, University of Bialystok, Bialystok, Poland
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Jaafar NR, Littler D, Beddoe T, Rossjohn J, Illias RM, Mahadi NM, Mackeen MM, Murad AMA, Abu Bakar FD. Crystal structure of fuculose aldolase from the Antarctic psychrophilic yeast Glaciozyma antarctica PI12. Acta Crystallogr F Struct Biol Commun 2016; 72:831-839. [PMID: 27827354 PMCID: PMC5101584 DOI: 10.1107/s2053230x16015612] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/04/2016] [Indexed: 11/11/2022] Open
Abstract
Fuculose-1-phosphate aldolase (FucA) catalyses the reversible cleavage of L-fuculose 1-phosphate to dihydroxyacetone phosphate (DHAP) and L-lactaldehyde. This enzyme from mesophiles and thermophiles has been extensively studied; however, there is no report on this enzyme from a psychrophile. In this study, the gene encoding FucA from Glaciozyma antarctica PI12 (GaFucA) was cloned and the enzyme was overexpressed in Escherichia coli, purified and crystallized. The tetrameric structure of GaFucA was determined to 1.34 Å resolution. The overall architecture of GaFucA and its catalytically essential histidine triad are highly conserved among other fuculose aldolases. Comparisons of structural features between GaFucA and its mesophilic and thermophilic homologues revealed that the enzyme has typical psychrophilic attributes, indicated by the presence of a high number of nonpolar residues at the surface and a lower number of arginine residues.
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Affiliation(s)
- Nardiah Rizwana Jaafar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor Darul Ehsan 43600, Malaysia
| | - Dene Littler
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
| | - Travis Beddoe
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
- Department of Animal Plant and Soil Science and Centre for AgriBioscience (AgriBio), La Trobe University, Melbourne Victoria 3086, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales
| | - Rosli Md Illias
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Darul Takzim, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Jalan Bangi Lama, 43000 Kajang, Selangor Darul Ehsan, Malaysia
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
| | - Mukram Mohamed Mackeen
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
- School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor Darul Ehsan 43600, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor Darul Ehsan 43600, Malaysia
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12
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Thorvaldsen S. A Mutation Model from First Principles of the Genetic Code. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:878-886. [PMID: 26485722 DOI: 10.1109/tcbb.2015.2489641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The paper presents a neutral Codons Probability Mutations (CPM) model of molecular evolution and genetic decay of an organism. The CPM model uses a Markov process with a 20-dimensional state space of probability distributions over amino acids. The transition matrix of the Markov process includes the mutation rate and those single point mutations compatible with the genetic code. This is an alternative to the standard Point Accepted Mutation (PAM) and BLOcks of amino acid SUbstitution Matrix (BLOSUM). Genetic decay is quantified as a similarity between the amino acid distribution of proteins from a (group of) species on one hand, and the equilibrium distribution of the Markov chain on the other. Amino acid data for the eukaryote, bacterium, and archaea families are used to illustrate how both the CPM and PAM models predict their genetic decay towards the equilibrium value of 1. A family of bacteria is studied in more detail. It is found that warm environment organisms on average have a higher degree of genetic decay compared to those species that live in cold environments. The paper addresses a new codon-based approach to quantify genetic decay due to single point mutations compatible with the genetic code. The present work may be seen as a first approach to use codon-based Markov models to study how genetic entropy increases with time in an effectively neutral biological regime. Various extensions of the model are also discussed.
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13
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Baweja M, Nain L, Kawarabayasi Y, Shukla P. Current Technological Improvements in Enzymes toward Their Biotechnological Applications. Front Microbiol 2016; 7:965. [PMID: 27379087 PMCID: PMC4909775 DOI: 10.3389/fmicb.2016.00965] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/03/2016] [Indexed: 01/07/2023] Open
Abstract
Enzymes from extremophiles are creating interest among researchers due to their unique properties and the enormous power of catalysis at extreme conditions. Since community demands are getting more intensified, therefore, researchers are applying various approaches viz. metagenomics to increase the database of extremophilic species. Furthermore, the innovations are being made in the naturally occurring enzymes utilizing various tools of recombinant DNA technology and protein engineering, which allows redesigning of the enzymes for its better fitment into the process. In this review, we discuss the biochemical constraints of psychrophiles during survival at the lower temperature. We summarize the current knowledge about the sources of such enzymes and their in vitro modification through mutagenesis to explore their biotechnological potential. Finally, we recap the microbial cell surface display to enhance the efficiency of the process in cost effective way.
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Affiliation(s)
- Mehak Baweja
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi India
| | - Yutaka Kawarabayasi
- National Institute of Advanced Industrial Science and Technology, Tsukuba Japan
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak India
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Shain DH, Halldórsdóttir K, Pálsson F, Aðalgeirsdóttir G, Gunnarsson A, Jónsson Þ, Lang SA, Pálsson HS, Steinþórssson S, Arnason E. Colonization of maritime glacier ice by bdelloid Rotifera. Mol Phylogenet Evol 2016; 98:280-7. [DOI: 10.1016/j.ympev.2016.02.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/22/2016] [Accepted: 02/22/2016] [Indexed: 11/26/2022]
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Moreno Switt AI, Andrus AD, Ranieri ML, Orsi RH, Ivy R, den Bakker HC, Martin NH, Wiedmann M, Boor KJ. Genomic comparison of sporeforming bacilli isolated from milk. BMC Genomics 2014; 15:26. [PMID: 24422886 PMCID: PMC3902026 DOI: 10.1186/1471-2164-15-26] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 01/08/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Sporeformers in the order Bacillales are important contributors to spoilage of pasteurized milk. While only a few Bacillus and Viridibacillus strains can grow in milk at 6°C, the majority of Paenibacillus isolated from pasteurized fluid milk can grow under these conditions. To gain a better understanding of genomic features of these important spoilage organisms and to identify candidate genomic features that may facilitate cold growth in milk, we performed a comparative genomic analysis of selected dairy associated sporeformers representing isolates that can and cannot grow in milk at 6°C. RESULTS The genomes for seven Paenibacillus spp., two Bacillus spp., and one Viridibacillus sp. isolates were sequenced. Across the genomes sequenced, we identified numerous genes encoding antimicrobial resistance mechanisms, bacteriocins, and pathways for synthesis of non-ribosomal peptide antibiotics. Phylogenetic analysis placed genomes representing Bacillus, Paenibacillus and Viridibacillus into three distinct well supported clades and further classified the Paenibacillus strains characterized here into three distinct clades, including (i) clade I, which contains one strain able to grow at 6°C in skim milk broth and one strain not able to grow under these conditions, (ii) clade II, which contains three strains able to grow at 6°C in skim milk broth, and (iii) clade III, which contains two strains unable to grow under these conditions. While all Paenibacillus genomes were found to include multiple copies of genes encoding β-galactosidases, clade II strains showed significantly higher numbers of genes encoding these enzymes as compared to clade III strains. Genome comparison of strains able to grow at 6°C and strains unable to grow at this temperature identified numerous genes encoding features that might facilitate the growth of Paenibacillus in milk at 6°C, including peptidases with cold-adapted features (flexibility and disorder regions in the protein structure) and cold-adaptation related proteins (DEAD-box helicases, chaperone DnaJ). CONCLUSIONS Through a comparative genomics approach we identified a number of genomic features that may relate to the ability of selected Paenibacillus strains to cause spoilage of refrigerated fluid milk. With additional experimental evidence, these data will facilitate identification of targets to detect and control Gram positive spore formers in fluid milk.
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Affiliation(s)
- Andrea I Moreno Switt
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Alexis D Andrus
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Matthew L Ranieri
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Renato H Orsi
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Reid Ivy
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Henk C den Bakker
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Kathryn J Boor
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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