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Galisteo C, de la Haba RR, Ventosa A, Sánchez-Porro C. The Hypersaline Soils of the Odiel Saltmarshes Natural Area as a Source for Uncovering a New Taxon: Pseudidiomarina terrestris sp. nov. Microorganisms 2024; 12:375. [PMID: 38399779 PMCID: PMC10893183 DOI: 10.3390/microorganisms12020375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The hypersaline soils of the Odiel Saltmarshes Natural Area are an extreme environment with high levels of some heavy metals; however, it is a relevant source of prokaryotic diversity that we aim to explore. In this study, six strains related to the halophilic genus Pseudidiomarina were isolated from this habitat. The phylogenetic study based on the 16S rRNA gene sequence and the fingerprinting analysis suggested that they constituted a single new species within the genus Pseudidiomarina. Comparative genomic analysis based on the OGRIs indices and the phylogeny inferred from the core genome were performed considering all the members of the family Idiomarinaceae. Additionally, a completed phenotypic characterization, as well as the fatty acid profile, were also carried out. Due to the characteristics of the habitat, genomic functions related to salinity and high heavy metal concentrations were studied, along with the global metabolism of the six isolates. Last, the ecological distribution of the isolates was studied in different hypersaline environments by genome recruitment. To sum up, the six strains constitute a new species within the genus Pseudidiomarina, for which the name Pseudidiomarina terrestris sp. nov. is proposed. The low abundance in all the studied hypersaline habitats indicates that it belongs to the rare biosphere in these habitats. In silico genome functional analysis suggests the presence of heavy metal transporters and pathways for nitrate reduction and nitrogen assimilation in low availability, among other metabolic traits.
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Affiliation(s)
| | | | | | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain; (C.G.); (R.R.d.l.H.); (A.V.)
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2
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Yao H, Liu S, Liu T, Ren D, Zhou Z, Yang Q, Mao J. Microbial-derived salt-tolerant proteases and their applications in high-salt traditional soybean fermented foods: a review. BIORESOUR BIOPROCESS 2023; 10:82. [PMID: 38647906 PMCID: PMC10992980 DOI: 10.1186/s40643-023-00704-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/31/2023] [Indexed: 04/25/2024] Open
Abstract
Different microorganisms can produce different proteases, which can adapt to different industrial requirements such as pH, temperature, and pressure. Salt-tolerant proteases (STPs) from microorganisms exhibit higher salt tolerance, wider adaptability, and more efficient catalytic ability under extreme conditions compared to conventional proteases. These unique enzymes hold great promise for applications in various industries including food, medicine, environmental protection, agriculture, detergents, dyes, and others. Scientific studies on microbial-derived STPs have been widely reported, but there has been little systematic review of microbial-derived STPs and their application in high-salt conventional soybean fermentable foods. This review presents the STP-producing microbial species and their selection methods, and summarizes and analyzes the salt tolerance mechanisms of the microorganisms. It also outlines various techniques for the isolation and purification of STPs from microorganisms and discusses the salt tolerance mechanisms of STPs. Furthermore, this review demonstrates the contribution of modern biotechnology in the screening of novel microbial-derived STPs and their improvement in salt tolerance. It highlights the potential applications and commercial value of salt-tolerant microorganisms and STPs in high-salt traditional soy fermented foods. The review ends with concluding remarks on the challenges and future directions for microbial-derived STPs. This review provides valuable insights into the separation, purification, performance enhancement, and application of microbial-derived STPs in traditional fermented foods.
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Affiliation(s)
- Hongli Yao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Department of Biology and Food Engineering, Bozhou University, Bozhou, 236800, Anhui, China
| | - Shuangping Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Tiantian Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Dongliang Ren
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Zhilei Zhou
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Qilin Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Jian Mao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China.
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China.
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China.
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3
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Zou D, Chen J, Zhang C, Kao SJ, Liu H, Li M. Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China. Appl Microbiol Biotechnol 2023; 107:6897-6909. [PMID: 37702790 DOI: 10.1007/s00253-023-12761-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/22/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.
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Affiliation(s)
- Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361000, China
| | - Hongbin Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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Kusebauch U, Lorenzetti APR, Campbell DS, Pan M, Shteynberg D, Kapil C, Midha MK, López García de Lomana A, Baliga NS, Moritz RL. A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS. Sci Data 2023; 10:697. [PMID: 37833331 PMCID: PMC10575869 DOI: 10.1038/s41597-023-02590-5] [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: 06/23/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish, E. coli and few other organisms. However, a spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotated H. salinarum NRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon. Data and spectral assay libraries are available via ProteomeXchange (PXD042770, PXD042774) and SWATHAtlas (SAL00312-SAL00319).
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Affiliation(s)
- Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | | | - David S Campbell
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Min Pan
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - David Shteynberg
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Charu Kapil
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Mukul K Midha
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Adrián López García de Lomana
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Nitin S Baliga
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
- Departments of Biology and Microbiology, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA.
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5
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Abstract
Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review the literature concerning habitat transitions among a variety of bacterial and archaeal lineages, considering the frequency of migration events, potential environmental barriers, and mechanisms of adaptation to new physicochemical conditions, including the modification of protein inventories and other genomic characteristics. Cells dependent on microbial hosts, particularly bacteria from the Candidate Phyla Radiation, have undergone repeated habitat transitions from environmental sources into animal microbiomes. We compare their trajectories to those of both free-living cells-including the Melainabacteria, Elusimicrobia, and methanogenic archaea-and cellular endosymbionts and bacteriophages, which have made similar transitions. We conclude by highlighting major related topics that may be worthy of future study.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Cindy J Castelle
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
| | - Jillian F Banfield
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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6
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Liang H, Song ZM, Zhong Z, Zhang D, Yang W, Zhou L, Older EA, Li J, Wang H, Zeng Z, Li YX. Genomic and metabolic analyses reveal antagonistic lanthipeptides in archaea. MICROBIOME 2023; 11:74. [PMID: 37060102 PMCID: PMC10105419 DOI: 10.1186/s40168-023-01521-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/16/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Microbes produce diverse secondary metabolites (SMs) such as signaling molecules and antimicrobials that mediate microbe-microbe interaction. Archaea, the third domain of life, are a large and diverse group of microbes that not only exist in extreme environments but are abundantly distributed throughout nature. However, our understanding of archaeal SMs lags far behind our knowledge of those in bacteria and eukarya. RESULTS Guided by genomic and metabolic analysis of archaeal SMs, we discovered two new lanthipeptides with distinct ring topologies from a halophilic archaeon of class Haloarchaea. Of these two lanthipeptides, archalan α exhibited anti-archaeal activities against halophilic archaea, potentially mediating the archaeal antagonistic interactions in the halophilic niche. To our best knowledge, archalan α represents the first lantibiotic and the first anti-archaeal SM from the archaea domain. CONCLUSIONS Our study investigates the biosynthetic potential of lanthipeptides in archaea, linking lanthipeptides to antagonistic interaction via genomic and metabolic analyses and bioassay. The discovery of these archaeal lanthipeptides is expected to stimulate the experimental study of poorly characterized archaeal chemical biology and highlight the potential of archaea as a new source of bioactive SMs. Video Abstract.
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Affiliation(s)
- Haoyu Liang
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhi-Man Song
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou, 515031, China
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dengwei Zhang
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Wei Yang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Le Zhou
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Ethan A Older
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Zhirui Zeng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
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Isolation of a virus causing a chronic infection in the archaeal model organism Haloferax volcanii reveals antiviral activities of a provirus. Proc Natl Acad Sci U S A 2022; 119:e2205037119. [PMID: 35994644 PMCID: PMC9436352 DOI: 10.1073/pnas.2205037119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses are important ecological, biogeochemical, and evolutionary drivers in every environment. Upon infection, they often cause the lysis of the host cell. However, some viruses exhibit alternative life cycles, such as chronic infections without cell lysis. The nature and the impact of chronic infections in prokaryotic host organisms remains largely unknown. Here, we characterize a novel haloarchaeal virus, Haloferax volcanii pleomorphic virus 1 (HFPV-1), which is currently the only virus infecting the model haloarchaeon Haloferax volcanii DS2, and demonstrate that HFPV-1 and H. volcanii are a great model system to study virus-host interactions in archaea. HFPV-1 is a pleomorphic virus that causes a chronic infection with continuous release of virus particles, but host and virus coexist without cell lysis or the appearance of resistant cells. Despite an only minor impact of the infection on host growth, we uncovered an extensive remodeling of the transcriptional program of the host (up to 1,049 differentially expressed genes). These changes are highlighted by a down-regulation of two endogenous provirus regions in the host genome, and we show that HFPV-1 infection is strongly influenced by a cross-talk between HFPV-1 and one of the proviruses mediated by a superinfection-like exclusion mechanism. Furthermore, HFPV-1 has a surprisingly wide host range among haloarchaea, and purified virus DNA can cause an infection after transformation into the host, making HFPV-1 a candidate for being developed into a genetic tool for a range of so far inaccessible haloarchaea.
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Salwan R, Sharma V. Genomics of Prokaryotic Extremophiles to Unfold the Mystery of Survival in Extreme Environments. Microbiol Res 2022; 264:127156. [DOI: 10.1016/j.micres.2022.127156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 11/26/2022]
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Mapping Archaeal Diversity in Soda Lakes by Coupling 16S rRNA PCR-DGGE Analysis with Remote Sensing and GIS Technology. FERMENTATION 2022. [DOI: 10.3390/fermentation8080365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The haloarchaeal diversity of four hypersaline alkaline lakes from the Wadi El-Natrun depression (Northern Egypt) was investigated using culture-independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene phylotypes, which was combined with remote sensing and geographic information system (GIS) data to highlight the distribution pattern of the microbial diversity in water and sediment samples. The majority of archaeal sequences identified in all four lakes belonged to the phyla Euryarchaeota and Crenarchaeota. Sediment samples from Beida Lake and water samples from El-Hamra Lake showed the highest levels of archaeal diversity. Sequence similarities ≥ 95% were found between six of the acquired clones and uncultured Halorhabdus, Euryarchaeota, and archaeon clones. In addition, two clones shared a high level of sequence similarity (97%) with unclassified archaea, while other nine clones exhibited 96% to 99% sequence similarity with uncultured archaeon clones, and only one clone showed 97% identity with an uncultured Crenarchaeota. Likewise, 7 DGGE bands presented a sequence similarity of 90 to 98% to Halogranum sp., Halalkalicoccus tibetensis, Halalkalicoccus jeotgali, uncultured Halorubrum, Halobacteriaceae sp., or uncultured haloarchaeon. In conclusion, while the variety of alkaliphilic haloarchaea in the examined soda lakes was restricted, the possibility of uncovering novel species for biotechnological applications from these extreme habitats remains promising.
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10
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Oliver JAW, Kelbrick M, Ramkissoon NK, Dugdale A, Stephens BP, Kucukkilic-Stephens E, Fox-Powell MG, Schwenzer SP, Antunes A, Macey MC. Sulfur Cycling as a Viable Metabolism under Simulated Noachian/Hesperian Chemistries. Life (Basel) 2022; 12:life12040523. [PMID: 35455014 PMCID: PMC9024814 DOI: 10.3390/life12040523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 12/17/2022] Open
Abstract
Water present on the surface of early Mars (>3.0 Ga) may have been habitable. Characterising analogue environments and investigating the aspects of their microbiome best suited for growth under simulated martian chemical conditions is key to understanding potential habitability. Experiments were conducted to investigate the viability of microbes from a Mars analogue environment, Colour Peak Springs (Axel Heiberg Island, Canadian High Arctic), under simulated martian chemistries. The fluid was designed to emulate waters thought to be typical of the late Noachian, in combination with regolith simulant material based on two distinct martian geologies. These experiments were performed with a microbial community from Colour Peak Springs sediment. The impact on the microbes was assessed by cell counting and 16S rRNA gene amplicon sequencing. Changes in fluid chemistries were tested using ICP-OES. Both chemistries were shown to be habitable, with growth in both chemistries. Microbial communities exhibited distinct growth dynamics and taxonomic composition, comprised of sulfur-cycling bacteria, represented by either sulfate-reducing or sulfur-oxidising bacteria, and additional heterotrophic halophiles. Our data support the identification of Colour Peak Springs as an analogue for former martian environments, with a specific subsection of the biota able to survive under more accurate proxies for martian chemistries.
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Affiliation(s)
- James A. W. Oliver
- Biology Department, Edge Hill University, Ormskirk L39 4QP, UK; (J.A.W.O.); (M.K.)
| | - Matthew Kelbrick
- Biology Department, Edge Hill University, Ormskirk L39 4QP, UK; (J.A.W.O.); (M.K.)
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3GJ, UK
| | - Nisha K. Ramkissoon
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - Amy Dugdale
- AstrobiologyOU, School of Physical Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK;
- Biology Department, Maynooth University, Maynooth, W23 F2H6 Kildare, Ireland
| | - Ben P. Stephens
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - Ezgi Kucukkilic-Stephens
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - Mark G. Fox-Powell
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
- School of Earth & Environmental Sciences, University of St Andrews, Fife KY16 9AJ, UK
| | - Susanne P. Schwenzer
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, China;
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Macau, China
| | - Michael C. Macey
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (N.K.R.); (B.P.S.); (E.K.-S.); (M.G.F.-P.); (S.P.S.)
- Correspondence:
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11
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Najjari A, Stathopoulou P, Elmnasri K, Hasnaoui F, Zidi I, Sghaier H, Ouzari HI, Cherif A, Tsiamis G. Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia. BIOLOGY 2021; 10:biology10050397. [PMID: 34064384 PMCID: PMC8147861 DOI: 10.3390/biology10050397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/27/2022]
Abstract
A thorough assessment of the phylogenetic diversity and community structure of halophilic archaea from three halite-crystal salts, processed from two separated saline systems of Southern Tunisia has been performed using culture dependent and independent methods targeting different regions of 16S rRNA gene sequences including DGGE, 16S rRNA clone libraries and Illumina Miseq sequencing. Two samples, CDR (red halite-crystal salts) and CDW (white halite-crystal salts), were collected from Chott-Eljerid and one sample CDZ (white halite-crystal salts) from Chott Douz. Fourteen isolates were identified as Halorubrum, Haloferax, Haloarcula, and Halogeometricum genera members. Culture-independent approach revealed a high diversity of archaeal members present in all samples, represented by the Euryarchaeal phylum and the dominance of the Halobacteria class. Nanohaloarchaea were also identified only in white halite samples based on metagenomic analysis. In fact, a total of 61 genera were identified with members of the Halorhabdus, Halonotius, Halorubrum, Haloarcula, and unclassified. Halobacteriaceae were shared among all samples. Unexpected diversity profiles between samples was observed where the red halite crust sample was considered as the most diverse one. The highest diversity was observed with Miseq approach, nevertheless, some genera were detected only with 16S rRNA clone libraries and cultured approaches.
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Affiliation(s)
- Afef Najjari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
- Correspondence:
| | - Panagiota Stathopoulou
- Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece; (P.S.); (G.T.)
| | - Khaled Elmnasri
- Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia; (K.E.); (H.S.); (A.C.)
| | - Faten Hasnaoui
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
| | - Ines Zidi
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
| | - Haitham Sghaier
- Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia; (K.E.); (H.S.); (A.C.)
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), 2020 Sidi Thabet, Tunisia
| | - Hadda Imene Ouzari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
| | - Ameur Cherif
- Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia; (K.E.); (H.S.); (A.C.)
| | - George Tsiamis
- Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece; (P.S.); (G.T.)
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12
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Zuo Z, Zhao D, Zhou J, Han J, Xiang H. Halalkalirubrum salinum gen. nov., sp. nov., a halophilic archaeon isolated from a saline lake. Antonie van Leeuwenhoek 2021; 114:83-94. [PMID: 33389352 DOI: 10.1007/s10482-020-01502-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/22/2020] [Indexed: 10/22/2022]
Abstract
A novel extremely halophilic archaeon, strain N1521T, was isolated from a saline lake in Tibet, China. Cells of the strain were pleomorphic and Gram-stain-negative. It produced red pigments. Growth was observed at 4-42 °C (optimum, 37 °C), pH 7.0-10.5 (optimum, 8.0-9.5), NaCl 11%-25% (optimum, 15%) and in the presence of 0-0.1 M MgCl2 (optimum, 0.05 M) in aerobic conditions. The minimum NaCl concentration that prevented cell lysis was 2% (w/v). The major polar lipids of strain N1521T were phosphatidylglycerol sulfate, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol and an unidentified glycolipid. The DNA G + C content was 58.37 mol%. According to 16S rRNA gene sequence comparisons, strain N1521T revealed the highest sequence similarity to Haloprofundus halophilus NK23T (91.38%) and Halogranum amylolyticum TNN58T (91.00%), and low sequence similarities (< 91%) with other genera in the order Haloferacales. Phylogenetic analysis based on the 16S rRNA gene and rpoB' gene sequence showed that strain N1521T was distinct from the members of the order Haloferacales. The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values calculated from whole genome-sequence comparison between strain N1521T and the members of the order Haloferacales were in the ranges of 15.1-18.2%, 68.8-73.0%, and 58.4-63.9%, respectively. Phylogenetic tree reconstructions based on the whole-genome sequences revealed that strain N1521T was closer to the members of the family Halorubraceae. Based on the data obtained, strain N1521T is thus considered to represent a novel species of a new genus within the family Halorubraceae, for which the name Halalkalirubrum salinum gen. nov., sp. nov. is proposed. The type strain is N1521T (= CGMCC 1.16693 = JCM 33785).
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Affiliation(s)
- Zhenqiang Zuo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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13
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He M, Xiong Y, Cheng K. Characters of a nitrobacter enrichment culture from a freshwater aquaculture pond. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1974944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Mengying He
- Hubei Key Laboratory of Ecological Restoration for River-Lakes and Algal Utilization, College of Resources and Environmental Engineering, Hubei University of Technology, Wuhan, Hubei, PR China
| | - Ying Xiong
- Hubei Key Laboratory of Ecological Restoration for River-Lakes and Algal Utilization, College of Resources and Environmental Engineering, Hubei University of Technology, Wuhan, Hubei, PR China
| | - Kai Cheng
- Hubei Key Laboratory of Ecological Restoration for River-Lakes and Algal Utilization, College of Resources and Environmental Engineering, Hubei University of Technology, Wuhan, Hubei, PR China
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14
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Tonner PD, Darnell CL, Bushell FML, Lund PA, Schmid AK, Schmidler SC. A Bayesian non-parametric mixed-effects model of microbial growth curves. PLoS Comput Biol 2020; 16:e1008366. [PMID: 33104703 PMCID: PMC7644099 DOI: 10.1371/journal.pcbi.1008366] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 11/05/2020] [Accepted: 08/30/2020] [Indexed: 11/19/2022] Open
Abstract
Substantive changes in gene expression, metabolism, and the proteome are manifested in overall changes in microbial population growth. Quantifying how microbes grow is therefore fundamental to areas such as genetics, bioengineering, and food safety. Traditional parametric growth curve models capture the population growth behavior through a set of summarizing parameters. However, estimation of these parameters from data is confounded by random effects such as experimental variability, batch effects or differences in experimental material. A systematic statistical method to identify and correct for such confounding effects in population growth data is not currently available. Further, our previous work has demonstrated that parametric models are insufficient to explain and predict microbial response under non-standard growth conditions. Here we develop a hierarchical Bayesian non-parametric model of population growth that identifies the latent growth behavior and response to perturbation, while simultaneously correcting for random effects in the data. This model enables more accurate estimates of the biological effect of interest, while better accounting for the uncertainty due to technical variation. Additionally, modeling hierarchical variation provides estimates of the relative impact of various confounding effects on measured population growth.
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Affiliation(s)
- Peter D. Tonner
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
- Biology Department, Duke University, Durham, NC, USA
| | | | - Francesca M. L. Bushell
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter A. Lund
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Amy K. Schmid
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
- Biology Department, Duke University, Durham, NC, USA
- Center for Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
| | - Scott C. Schmidler
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
- Department of Statistical Science, Duke University, Durham, USA
- Department of Computer Science, Duke University, Durham, USA
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Verma DK, Vasudeva G, Sidhu C, Pinnaka AK, Prasad SE, Thakur KG. Biochemical and Taxonomic Characterization of Novel Haloarchaeal Strains and Purification of the Recombinant Halotolerant α-Amylase Discovered in the Isolate. Front Microbiol 2020; 11:2082. [PMID: 32983058 PMCID: PMC7490331 DOI: 10.3389/fmicb.2020.02082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/07/2020] [Indexed: 11/13/2022] Open
Abstract
Haloarchaea are salt-loving archaea and potential source of industrially relevant halotolerant enzymes. In the present study, three reddish-pink, extremely halophilic archaeal strains, namely wsp1 (wsp-water sample Pondicherry), wsp3, and wsp4, were isolated from the Indian Solar saltern. The phylogenetic analysis based on 16S rRNA gene sequences suggests that both wsp3 and wsp4 strains belong to Halogeometricum borinquense while wsp1 is closely related to Haloferax volcanii species. The comparative genomics revealed an open pangenome for both genera investigated here. Whole-genome sequence analysis revealed that these isolates have multiple copies of industrially/biotechnologically important unique genes and enzymes. Among these unique enzymes, for recombinant expression and purification, we selected four putative α-amylases identified in these three isolates. We successfully purified functional halotolerant recombinant Amy2, from wsp1 using pelB signal sequence-based secretion strategy using Escherichia coli as an expression host. This method may prove useful to produce functional haloarchaeal secretory recombinant proteins suitable for commercial or research applications. Biochemical analysis of Amy2 suggests the halotolerant nature of the enzyme having maximum enzymatic activity observed at 1 M NaCl. We also report the isolation and characterization of carotenoids purified from these isolates. This study highlights the presence of several industrially important enzymes in the haloarchaeal strains which may potentially have improved features like stability and salt tolerance suitable for industrial applications.
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Affiliation(s)
- Dipesh Kumar Verma
- G. N. Ramachandran Protein Centre, Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Gunjan Vasudeva
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Chandni Sidhu
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Anil K Pinnaka
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Senthil E Prasad
- Biochemical Engineering Research and Process Development Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Krishan Gopal Thakur
- G. N. Ramachandran Protein Centre, Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
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16
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Wang Y, Huang JM, Zhou YL, Almeida A, Finn RD, Danchin A, He LS. Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli. BMC Genomics 2020; 21:408. [PMID: 32552739 PMCID: PMC7301438 DOI: 10.1186/s12864-020-06807-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/05/2020] [Indexed: 12/28/2022] Open
Abstract
Background The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. Results Several environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. Conclusions This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.
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Affiliation(s)
- Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.
| | - Jiao-Mei Huang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Alexandre Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Antoine Danchin
- Kodikos, Department of Infection, Immunity and Inflammation, Institut Cochin INSERM U1016 - CNRS UMR8104 - Université Paris Descartes, 24 rue du Faubourg Saint-Jacques, 75014, Paris, France.,Li Kashing Faculty of Medicine, School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong, SAR, China
| | - Li-Sheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China
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17
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Pfeiffer F, Losensky G, Marchfelder A, Habermann B, Dyall‐Smith M. Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754 T ) and the laboratory strains R1 and NRC-1. Microbiologyopen 2020; 9:e974. [PMID: 31797576 PMCID: PMC7002104 DOI: 10.1002/mbo3.974] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 01/04/2023] Open
Abstract
Halobacterium salinarum is an extremely halophilic archaeon that is widely distributed in hypersaline environments and was originally isolated as a spoilage organism of salted fish and hides. The type strain 91-R6 (DSM 3754T ) has seldom been studied and its genome sequence has only recently been determined by our group. The exact relationship between the type strain and two widely used model strains, NRC-1 and R1, has not been described before. The genome of Hbt. salinarum strain 91-R6 consists of a chromosome (2.17 Mb) and two large plasmids (148 and 102 kb, with 39,230 bp being duplicated). Cytosine residues are methylated (m4 C) within CTAG motifs. The genomes of type and laboratory strains are closely related, their chromosomes sharing average nucleotide identity (ANIb) values of 98% and in silico DNA-DNA hybridization (DDH) values of 95%. The chromosomes are completely colinear, do not show genome rearrangement, and matching segments show <1% sequence difference. Among the strain-specific sequences are three large chromosomal replacement regions (>10 kb). The well-studied AT-rich island (61 kb) of the laboratory strains is replaced by a distinct AT-rich sequence (47 kb) in 91-R6. Another large replacement (91-R6: 78 kb, R1: 44 kb) codes for distinct homologs of proteins involved in motility and N-glycosylation. Most (107 kb) of plasmid pHSAL1 (91-R6) is very closely related to part of plasmid pHS3 (R1) and codes for essential genes (e.g. arginine-tRNA ligase and the pyrimidine biosynthesis enzyme aspartate carbamoyltransferase). Part of pHS3 (42.5 kb total) is closely related to the largest strain-specific sequence (164 kb) in the type strain chromosome. Genome sequencing unraveled the close relationship between the Hbt. salinarum type strain and two well-studied laboratory strains at the DNA and protein levels. Although an independent isolate, the type strain shows a remarkably low evolutionary difference to the laboratory strains.
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Affiliation(s)
- Friedhelm Pfeiffer
- Computational Biology GroupMax‐Planck‐Institute of BiochemistryMartinsriedGermany
| | - Gerald Losensky
- Microbiology and ArchaeaDepartment of BiologyTechnische Universität DarmstadtDarmstadtGermany
| | | | - Bianca Habermann
- Computational Biology GroupMax‐Planck‐Institute of BiochemistryMartinsriedGermany
- CNRSIBDM UMR 7288Aix Marseille UniversitéMarseilleFrance
| | - Mike Dyall‐Smith
- Computational Biology GroupMax‐Planck‐Institute of BiochemistryMartinsriedGermany
- Veterinary BiosciencesFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVic.Australia
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18
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Edbeib MF, Aksoy HM, Kaya Y, Wahab RA, Huyop F. Haloadaptation: insights from comparative modeling studies between halotolerant and non-halotolerant dehalogenases. J Biomol Struct Dyn 2019; 38:3452-3461. [PMID: 31422756 DOI: 10.1080/07391102.2019.1657498] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Halophiles are extremophilic microorganisms that grow optimally at high salt concentrations by producing a myriad of equally halotolerant enzymes. Structural haloadaptation of these enzymes adept to thriving under high-salt environments, though are not fully understood. Herein, the study attempts an in silico investigation to identify and comprehend the evolutionary structural adaptation of a halotolerant dehalogenase, DehHX (GenBank accession number: KR297065) of the halotolerant Pseudomonas halophila, over its non-halotolerant counterpart, DehMX1 (GenBank accession number KY129692) produced by Pseudomonas aeruginosa. GC content of the halotolerant DehHX DNA sequence was distinctively higher (58.9%) than the non-halotolerant dehalogenases (55% average GC). Its acidic residues, Asp and Glu were 8.27% and 12.06%, respectively, compared to an average 5.5% Asp and 7% Glu, in the latter; but lower contents of basic and hydrophobic residues in the DehHX. The secondary structure of DehHX interestingly revealed a lower incidence of α-helix forming regions (29%) and a higher percentage of coils (57%), compared to 49% and 29% in the non-halotolerant homologues, respectively. Simulation models showed the DehHX is stable under a highly saline environment (25% w/v) by adopting a highly negative-charged surface with a concomitant weakly interacting hydrophobic core. The study thus, established that a halotolerant dehalogenase undergoes notable evolutionary structural changes related to GC content over its non-halotolerant counterpart, in order to adapt and thrive under highly saline environments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed Faraj Edbeib
- Department of Animal Production, Faculty of Agriculture, Baniwalid University, Baniwalid, Libya.,Department of Plant Protection, Agricultural Faculty, Ondokuz Mayis University, Samsun, Turkey
| | - Hasan Murat Aksoy
- Department of Plant Protection, Agricultural Faculty, Ondokuz Mayis University, Samsun, Turkey
| | - Yilmaz Kaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey.,Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Fahrul Huyop
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey.,Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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19
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Nagel C, Machulla A, Zahn S, Soppa J. Several One-Domain Zinc Finger µ-Proteins of Haloferax Volcanii Are Important for Stress Adaptation, Biofilm Formation, and Swarming. Genes (Basel) 2019; 10:genes10050361. [PMID: 31083437 PMCID: PMC6562870 DOI: 10.3390/genes10050361] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 11/16/2022] Open
Abstract
Zinc finger domains are highly structured and can mediate interactions to DNA, RNA, proteins, lipids, and small molecules. Accordingly, zinc finger proteins are very versatile and involved in many biological functions. Eukaryotes contain a wealth of zinc finger proteins, but zinc finger proteins have also been found in archaea and bacteria. Large zinc finger proteins have been well studied, however, in stark contrast, single domain zinc finger µ-proteins of less than 70 amino acids have not been studied at all, with one single exception. Therefore, 16 zinc finger µ-proteins of the haloarchaeon Haloferax volcanii were chosen and in frame deletion mutants of the cognate genes were generated. The phenotypes of mutants and wild-type were compared under eight different conditions, which were chosen to represent various pathways and involve many genes. None of the mutants differed from the wild-type under optimal or near-optimal conditions. However, 12 of the 16 mutants exhibited a phenotypic difference under at least one of the four following conditions: Growth in synthetic medium with glycerol, growth in the presence of bile acids, biofilm formation, and swarming. In total, 16 loss of function and 11 gain of function phenotypes were observed. Five mutants indicated counter-regulation of a sessile versus a motile life style in H. volcanii. In conclusion, the generation and analysis of a set of deletion mutants demonstrated the high importance of zinc finger µ-proteins for various biological functions, and it will be the basis for future mechanistic insight.
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Affiliation(s)
- Chantal Nagel
- Department of Biosciences, Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.
| | - Anja Machulla
- Department of Biosciences, Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.
| | - Sebastian Zahn
- Department of Biosciences, Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.
| | - Jörg Soppa
- Department of Biosciences, Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.
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20
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Tschitschko B, Erdmann S, DeMaere MZ, Roux S, Panwar P, Allen MA, Williams TJ, Brazendale S, Hancock AM, Eloe-Fadrosh EA, Cavicchioli R. Genomic variation and biogeography of Antarctic haloarchaea. MICROBIOME 2018; 6:113. [PMID: 29925429 PMCID: PMC6011602 DOI: 10.1186/s40168-018-0495-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/06/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands). To assess variation in haloarchaeal populations, including the presence of genomic islands, metagenomes from six hypersaline Antarctic lakes were characterised. RESULTS The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strains' two smaller replicons (secondary replicons) were highly variable. Intergenera gene exchange was identified, including the sharing of a type I-B CRISPR system. Evaluation of infectivity of an Antarctic halovirus provided experimental evidence for the differential susceptibility of the strains, bolstering inferences that strain variation is important for modulating interactions with viruses. A relationship was found between genomic structuring and the location of variation within replicons and genomic islands, demonstrating that the way in which haloarchaea accommodate genomic variability relates to replicon structuring. Metagenome read and contig mapping and clustering and scaling analyses demonstrated biogeographical patterning of variation consistent with environment and distance effects. The metagenome data also demonstrated that specific haloarchaeal species dominated the hypersaline systems indicating they are endemic to Antarctica. CONCLUSION The study describes how genomic variation manifests in Antarctic-lake haloarchaeal communities and provides the basis for future assessments of Antarctic regional and global biogeography of haloarchaea.
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Affiliation(s)
- Bernhard Tschitschko
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present Address: Climate Change Cluster, Department of Environmental Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Susanne Erdmann
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Matthew Z DeMaere
- i3 Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Simon Roux
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- , Present Address: 476 Lancaster Rd, Pegarah, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present Address: University of Tasmania Institute of Marine and Antarctic Studies, Antarctic Gateway Partnership and Antarctic Climate and Ecosystem Research Centre, Battery Point, Tasmania, Australia
| | | | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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21
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Fox-Powell MG, Cockell CS. Building a Geochemical View of Microbial Salt Tolerance: Halophilic Adaptation of Marinococcus in a Natural Magnesium Sulfate Brine. Front Microbiol 2018; 9:739. [PMID: 29713317 PMCID: PMC5911959 DOI: 10.3389/fmicb.2018.00739] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/29/2018] [Indexed: 11/13/2022] Open
Abstract
Current knowledge of life in hypersaline habitats is mostly limited to sodium and chloride-dominated environments. This narrow compositional window does not reflect the diversity of brine environments that exist naturally on Earth and other planetary bodies. Understanding the limits of the microbial biosphere and predicting extraterrestrial habitability demands a systematic effort to characterize ionic specificities of organisms from a representative range of saline habitats. Here, we investigated a strain of Marinococcus isolated from the magnesium and sulfate-dominated Basque Lakes (British Columbia, Canada). This organism was the sole isolate obtained after exposure to exceptionally high levels of Mg2+ and SO42- ions (2.369 and 2.840 M, respectively), and grew at extremes of ionic strength not normally encountered in Na+/Cl- brines (12.141 mol liter-1). Its association at the 16S rDNA level with bacterial halophiles suggests that ancestral halophily has allowed it to adapt to a different saline habitat. Growth was demonstrated in media dominated by NaCl, Na2SO4, MgCl2, and MgSO4, yet despite this plasticity the strain was still restricted; requiring either Na+ or Cl- to maintain short doubling times. Water activity could not explain growth rate differences between media, demonstrating the importance of ionic composition for dictating microbial growth windows. A new framework for understanding growth in brines is required, that accounts for the geochemical history of brines as well as the various stresses that ions impose on microbes. Studies such as this are required to gain a truly universal understanding of the limits of biological ion tolerance.
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Affiliation(s)
- Mark G Fox-Powell
- UK Centre for Astrobiology, School of Physics and Astronomy, The University of Edinburgh, Edinburgh, United Kingdom.,School of Earth and Environmental Sciences, University of St Andrews, St Andrews, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, The University of Edinburgh, Edinburgh, United Kingdom
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22
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Gunde-Cimerman N, Plemenitaš A, Oren A. Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations. FEMS Microbiol Rev 2018. [DOI: 10.1093/femsre/fuy009] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Ana Plemenitaš
- Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 1, SI-1000 Ljubljana, Slovenia
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
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23
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Almeida-Dalmet S, Litchfield CD, Gillevet P, Baxter BK. Differential Gene Expression in Response to Salinity and Temperature in a Haloarcula Strain from Great Salt Lake, Utah. Genes (Basel) 2018; 9:genes9010052. [PMID: 29361787 PMCID: PMC5793203 DOI: 10.3390/genes9010052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 01/01/2023] Open
Abstract
Haloarchaea that inhabit Great Salt Lake (GSL), a thalassohaline terminal lake, must respond to the fluctuating climate conditions of the elevated desert of Utah. We investigated how shifting environmental factors, specifically salinity and temperature, affected gene expression in the GSL haloarchaea, NA6-27, which we isolated from the hypersaline north arm of the lake. Combined data from cultivation, microscopy, lipid analysis, antibiotic sensitivity, and 16S rRNA gene alignment, suggest that NA6-27 is a member of the Haloarcula genus. Our prior study demonstrated that archaea in the Haloarcula genus were stable in the GSL microbial community over seasons and years. In this study, RNA arbitrarily primed PCR (RAP-PCR) was used to determine the transcriptional responses of NA6-27 grown under suboptimal salinity and temperature conditions. We observed alteration of the expression of genes related to general stress responses, such as transcription, translation, replication, signal transduction, and energy metabolism. Of the ten genes that were expressed differentially under stress, eight of these genes responded in both conditions, highlighting this general response. We also noted gene regulation specific to salinity and temperature conditions, such as osmoregulation and transport. Taken together, these data indicate that the GSL Haloarcula strain, NA6-27, demonstrates both general and specific responses to salinity and/or temperature stress, and suggest a mechanistic model for homeostasis that may explain the stable presence of this genus in the community as environmental conditions shift.
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Affiliation(s)
- Swati Almeida-Dalmet
- Department of Environmental Science and Policy, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA.
| | - Carol D Litchfield
- Department of Environmental Science and Policy, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA.
| | - Patrick Gillevet
- Department of Biology, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA.
| | - Bonnie K Baxter
- Great Salt Lake Institute, Westminster College, 1840 South 1300 East, Salt Lake City, UT 84105, USA.
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24
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Luo H, Quan CL, Peng C, Gao F. Recent development of Ori-Finder system and DoriC database for microbial replication origins. Brief Bioinform 2018; 20:1114-1124. [DOI: 10.1093/bib/bbx174] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Indexed: 01/28/2023] Open
Abstract
Abstract
DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC. Ori-Finder system and DoriC database are currently used in the research field of DNA replication origins in prokaryotes, including: (i) identification of oriC regions in bacterial and archaeal genomes; (ii) discovery and analysis of the conserved sequences within oriC regions; and (iii) strand-biased analysis of bacterial genomes.
Up to now, more and more predicted results by Ori-Finder system were supported by subsequent experiments, and Ori-Finder system has been used to identify the replication origins in > 100 newly sequenced prokaryotes in their genome reports. In addition, the data in DoriC database have been widely used in the large-scale analyses of replication origins and strand bias in prokaryotic genomes. Here, we review the development of Ori-Finder system and DoriC database as well as their applications. Some future directions and aspects for extending the application of Ori-Finder and DoriC are also presented.
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25
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Gupta S, Roy M, Ghosh A. The Archaeal Signal Recognition Particle: Present Understanding and Future Perspective. Curr Microbiol 2016; 74:284-297. [DOI: 10.1007/s00284-016-1167-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 11/21/2016] [Indexed: 10/20/2022]
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26
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Williams TJ, Allen M, Tschitschko B, Cavicchioli R. Glycerol metabolism of haloarchaea. Environ Microbiol 2016; 19:864-877. [PMID: 27768817 DOI: 10.1111/1462-2920.13580] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Haloarchaea are heterotrophic members of the Archaea that thrive in hypersaline environments, often feeding off the glycerol that is produced as an osmolyte by eucaryotic Dunaliella during primary production. In this study we analyzed glycerol metabolism genes in closed genomes of haloarchaea and examined published data describing the growth properties of haloarchaea and experimental data for the enzymes involved. By integrating the genomic data with knowledge from the literature, we derived an understanding of the ecophysiology and evolutionary properties of glycerol catabolic pathways in haloarchaea.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Michelle Allen
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Bernhard Tschitschko
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
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27
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AglM and VNG1048G, Two Haloarchaeal UDP-Glucose Dehydrogenases, Show Different Salt-Related Behaviors. Life (Basel) 2016; 6:life6030031. [PMID: 27527219 PMCID: PMC5041007 DOI: 10.3390/life6030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 11/16/2022] Open
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28
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Jaakkola ST, Pfeiffer F, Ravantti JJ, Guo Q, Liu Y, Chen X, Ma H, Yang C, Oksanen HM, Bamford DH. The complete genome of a viable archaeum isolated from 123-million-year-old rock salt. Environ Microbiol 2016; 18:565-79. [DOI: 10.1111/1462-2920.13130] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 03/02/2015] [Accepted: 03/15/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Salla T. Jaakkola
- Department of Biosciences; Institute of Biotechnology; University of Helsinki; Helsinki Finland
| | - Friedhelm Pfeiffer
- Department of Membrane Biochemistry; Max Planck Institute of Biochemistry; München Germany
| | - Janne J. Ravantti
- Department of Biosciences; Institute of Biotechnology; University of Helsinki; Helsinki Finland
| | - Qinggong Guo
- State Key Laboratory of Virology; College of Life Sciences; Wuhan University; Wuhan China
| | - Ying Liu
- State Key Laboratory of Virology; College of Life Sciences; Wuhan University; Wuhan China
| | - Xiangdong Chen
- State Key Laboratory of Virology; College of Life Sciences; Wuhan University; Wuhan China
| | - Hongling Ma
- State Key Laboratory of Geomechanics and Geotechnical Engineering; Institute of Rock and Soil Mechanics; The Chinese Academy of Science; Wuhan China
| | - Chunhe Yang
- State Key Laboratory of Geomechanics and Geotechnical Engineering; Institute of Rock and Soil Mechanics; The Chinese Academy of Science; Wuhan China
| | - Hanna M. Oksanen
- Department of Biosciences; Institute of Biotechnology; University of Helsinki; Helsinki Finland
| | - Dennis H. Bamford
- Department of Biosciences; Institute of Biotechnology; University of Helsinki; Helsinki Finland
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29
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Wong HL, Ahmed-Cox A, Burns BP. Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions. Microorganisms 2016; 4:microorganisms4010006. [PMID: 27681900 PMCID: PMC5029511 DOI: 10.3390/microorganisms4010006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/08/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S’Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia.
- Australian Centre for Astrobiology, University of New South Wales, Sydney 2052, Australia.
| | - Aria Ahmed-Cox
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia.
| | - Brendan Paul Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia.
- Australian Centre for Astrobiology, University of New South Wales, Sydney 2052, Australia.
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30
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Gómez S, López-Estepa M, Fernández FJ, Vega MC. Protein Complex Production in Alternative Prokaryotic Hosts. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 896:115-33. [PMID: 27165322 DOI: 10.1007/978-3-319-27216-0_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Research for multiprotein expression in nonconventional bacterial and archaeal expression systems aims to exploit particular properties of "alternative" prokaryotic hosts that might make them more efficient than E. coli for particular applications, especially in those areas where more conventional bacterial hosts traditionally do not perform well. Currently, a wide range of products with clinical or industrial application have to be isolated from their native source, often microorganisms whose growth present numerous problems owing to very slow growth phenotypes or because they are unculturable under laboratory conditions. In those cases, transfer of the gene pathway responsible for synthesizing the product of interest into a suitable recombinant host becomes an attractive alternative solution. Despite many efforts dedicated to improving E. coli systems due to low cost, ease of use, and its dominant position as a ubiquitous expression host model, many alternative prokaryotic systems have been developed for heterologous protein expression mostly for biotechnological applications. Continuous research has led to improvements in expression yield through these non-conventional models, including Pseudomonas, Streptomyces and Mycobacterium as alternative bacterial expression hosts. Advantageous properties shared by these systems include low costs, high levels of secreted protein products and their safety of use, with non-pathogenic strains been commercialized. In addition, the use of extremophilic and halotolerant archaea as expression hosts has to be considered as a potential tool for the production of mammalian membrane proteins such as GPCRs.
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Affiliation(s)
- Sara Gómez
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Miguel López-Estepa
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Francisco J Fernández
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - M Cristina Vega
- Center for Biological Research, Spanish National Research Council (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
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31
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Derntl C, Selb R, Klein R, Alte B, Witte A. Genomic manipulations in alkaliphilic haloarchaea demonstrated by a gene disruption in Natrialba magadii. FEMS Microbiol Lett 2015; 362:fnv179. [PMID: 26424765 DOI: 10.1093/femsle/fnv179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2015] [Indexed: 11/14/2022] Open
Abstract
Alkaliphilic haloarchaea, a distinct physiological group from the closely related neutrophilic haloarchaea, represent an underutilized resource for basic research and industrial applications. In contrast to the neutrophilic haloarchaea, no reports on genomic manipulations in haloalkaliphiles have been published until now. Genomic manipulations via homologous recombination are useful for basic research. In this study, we demonstrate the possibility for this strategy in alkaliphilic haloarchaea for the first time. In a previous study, we developed a PEG-mediated transformation technique for alkaliphilic haloarchaea that was deployed in this study to deliver a gene disruption cassette into the model organism Natrialba magadii. The gene encoding for the well-studied Natrialba extracellular protease was successfully disrupted by a recombination marker gene, demonstrating a proof of principle for the usability of homologous recombination for genomic manipulations in alkaliphilic haloarchaea. Since halo(alkali)philic Archaea are polyploid, a selection process was applied in order to obtain a mutant strain containing exclusively disrupted genes. The resulting strain exhibited no proteolytic activity measurable by an azo-casein assay. Complementation was able to restore proteolytic activity. The expression pattern of the Natrialba extracellular protease was different in the complemented strain.
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Affiliation(s)
- Christian Derntl
- Department of Microbiology, Immunobiology and Genetics, MFPL Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Regina Selb
- Department of Microbiology, Immunobiology and Genetics, MFPL Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Reinhard Klein
- IMC FH Krems, University of Applied Sciences, Piaristengasse 1, 3500 Krems, Austria
| | - Beatrix Alte
- Department of Microbiology, Immunobiology and Genetics, MFPL Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Angela Witte
- Department of Microbiology, Immunobiology and Genetics, MFPL Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
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32
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High production of bacteriorhodopsin from wild type Halobacterium salinarum. Extremophiles 2015; 19:1021-8. [DOI: 10.1007/s00792-015-0778-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/23/2015] [Indexed: 11/26/2022]
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33
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Walker JE, Santangelo TJ. Analyses of in vivo interactions between transcription factors and the archaeal RNA polymerase. Methods 2015; 86:73-9. [PMID: 26028597 DOI: 10.1016/j.ymeth.2015.05.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/22/2015] [Accepted: 05/23/2015] [Indexed: 11/27/2022] Open
Abstract
Transcription factors regulate the activities of RNA polymerase (RNAP) at each stage of the transcription cycle. Many basal transcription factors with common ancestry are employed in eukaryotic and archaeal systems that directly bind to RNAP and influence intramolecular movements of RNAP and modulate DNA or RNA interactions. We describe and employ a flexible methodology to directly probe and quantify the binding of transcription factors to RNAP in vivo. We demonstrate that binding of the conserved and essential archaeal transcription factor TFE to the archaeal RNAP is directed, in part, by interactions with the RpoE subunit of RNAP. As the surfaces involved are conserved in many eukaryotic and archaeal systems, the identified TFE-RNAP interactions are likely conserved in archaeal-eukaryal systems and represent an important point of contact that can influence the efficiency of transcription initiation.
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Affiliation(s)
- Julie E Walker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
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34
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Bang C, Schmitz RA. Archaea associated with human surfaces: not to be underestimated. FEMS Microbiol Rev 2015; 39:631-48. [DOI: 10.1093/femsre/fuv010] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 12/18/2022] Open
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35
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Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. PLoS Genet 2014; 10:e1004784. [PMID: 25393412 PMCID: PMC4230888 DOI: 10.1371/journal.pgen.1004784] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/29/2014] [Indexed: 12/19/2022] Open
Abstract
Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes. The ability to adjust to changing osmotic conditions (osmoadaptation) is crucial to the survival of organisms across the tree of life. However, significant gaps still exist in our understanding of this important phenomenon. To help fill some of these gaps, we have produced high-quality draft genomes for 59 osmoadaptation “experts” (extreme halophiles of the euryarchaeal family Halobacteriaceae). We describe the dispersal of osmoadaptive protein families across the haloarchaeal evolutionary tree. We use this data to suggest a generalized model for haloarchaeal ion transport in response to changing osmotic conditions, including proposed new mechanisms for magnesium and chloride accumulation. We describe the evolutionary expansion and differentiation of haloarchaeal general transcription factor families and discuss their potential for enabling rapid adaptation to environmental fluxes. Lastly, we challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. This result highlights the power of our dataset for making evolutionary inferences, a feature which will make it useful to the broader evolutionary community. We distribute our genomic dataset through a user-friendly graphical interface.
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36
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Paggi RA, Giménez MI, De Castro RE, Cesari A. A simple technique to improve the resolution of membrane acidic proteins of the haloarchaeon Haloferax volcanii by 2D electrophoresis. Electrophoresis 2014; 35:3518-22. [PMID: 25224925 DOI: 10.1002/elps.201400407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 11/06/2022]
Abstract
Proteins present in the archaeal cell envelope play key roles in a variety of processes necessary for survival in extreme environments. The haloarchaeon Haloferax volcanii is a good model for membrane proteomic studies because its genome sequence is known, it can be genetically manipulated, and a number of studies at the "omics" level have been performed in this organism. This work reports an easy strategy to improve the resolution of acidic membrane proteins from H. volcanii by 2DE. The method is based on the solubilization, delipidation, and salt removal from membrane proteins. Due to the abundance of the S-layer glycoprotein (SLG) in membrane protein extracts, other proteins from the envelope are consequently underrepresented. Thus, a protocol to reduce the amount of the SLG by EDTA treatment was applied and 11 cm narrow range pH (3.9-5.1) IPG strips were used to fractionate the remaining proteins. Using this method, horizontal streaking was substantially decreased and at least 75 defined spots (20% of the predicted membrane proteome within this pI/Mw range) were reproducibly detected. Two of these spots were identified as thermosome subunit 1 and NADH dehydrogenase from H. volcanii, confirming that proteins from the membrane fraction were enriched. Removal of the SLG from membrane protein extracts can be applied to increase protein load for 2DE as well as for other proteomic methods.
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Affiliation(s)
- Roberto A Paggi
- Instituto de Investigaciones Biológicas, UNMdP-CONICET, Mar del Plata, Argentina
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Luo H, Zhang CT, Gao F. Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes. Front Microbiol 2014; 5:482. [PMID: 25309521 PMCID: PMC4164010 DOI: 10.3389/fmicb.2014.00482] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 08/27/2014] [Indexed: 11/13/2022] Open
Abstract
DNA replication is one of the most basic processes in all three domains of cellular life. With the advent of the post-genomic era, the increasing number of complete archaeal genomes has created an opportunity for exploration of the molecular mechanisms for initiating cellular DNA replication by in vivo experiments as well as in silico analysis. However, the location of replication origins (oriCs) in many sequenced archaeal genomes remains unknown. We present a web-based tool Ori-Finder 2 to predict oriCs in the archaeal genomes automatically, based on the integrated method comprising the analysis of base composition asymmetry using the Z-curve method, the distribution of origin recognition boxes identified by FIMO tool, and the occurrence of genes frequently close to oriCs. The web server is also able to analyze the unannotated genome sequences by integrating with gene prediction pipelines and BLAST software for gene identification and function annotation. The result of the predicted oriCs is displayed as an HTML table, which offers an intuitive way to browse the result in graphical and tabular form. The software presented here is accurate for the genomes with single oriC, but it does not necessarily find all the origins of replication for the genomes with multiple oriCs. Ori-Finder 2 aims to become a useful platform for the identification and analysis of oriCs in the archaeal genomes, which would provide insight into the replication mechanisms in archaea. The web server is freely available at http://tubic.tju.edu.cn/Ori-Finder2/.
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Affiliation(s)
- Hao Luo
- Department of Physics, Tianjin University Tianjin, China
| | | | - Feng Gao
- Department of Physics, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering Tianjin, China
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Chimileski S, Franklin MJ, Papke RT. Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer. BMC Biol 2014; 12:65. [PMID: 25124934 PMCID: PMC4180959 DOI: 10.1186/s12915-014-0065-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/31/2014] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Archaea share a similar microbial lifestyle with bacteria, and not surprisingly then, also exist within matrix-enclosed communities known as biofilms. Advances in biofilm biology have been made over decades for model bacterial species, and include characterizations of social behaviors and cellular differentiation during biofilm development. Like bacteria, archaea impact ecological and biogeochemical systems. However, the biology of archaeal biofilms is only now being explored. Here, we investigated the development, composition and dynamics of biofilms formed by the haloarchaeon Haloferax volcanii DS2. RESULTS Biofilms were cultured in static liquid and visualized with fluorescent cell membrane dyes and by engineering cells to express green fluorescent protein (GFP). Analysis by confocal scanning laser microscopy showed that H. volcanii cells formed microcolonies within 24 h, which developed into larger clusters by 48 h and matured into flake-like towers often greater than 100 μm in height after 7 days. To visualize the extracellular matrix, biofilms formed by GFP-expressing cells were stained with concanavalin A, DAPI, Congo red and thioflavin T. Stains colocalized with larger cellular structures and indicated that the extracellular matrix may contain a combination of polysaccharides, extracellular DNA and amyloid protein. Following a switch to biofilm growth conditions, a sub-population of cells differentiated into chains of long rods sometimes exceeding 25 μm in length, compared to their planktonic disk-shaped morphology. Time-lapse photography of static liquid biofilms also revealed wave-like social motility. Finally, we quantified gene exchange between biofilm cells, and found that it was equivalent to the mating frequency of a classic filter-based experimental method. CONCLUSIONS The developmental processes, functional properties and dynamics of H. volcanii biofilms provide insight on how haloarchaeal species might persist, interact and exchange DNA in natural communities. H. volcanii demonstrates some biofilm phenotypes similar to bacterial biofilms, but also has interesting phenotypes that may be unique to this organism or to this class of organisms, including changes in cellular morphology and an unusual form of social motility. Because H. volcanii has one of the most advanced genetic systems for any archaeon, the phenotypes reported here may promote the study of genetic and developmental processes in archaeal biofilms.
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Fernández AB, Vera-Gargallo B, Sánchez-Porro C, Ghai R, Papke RT, Rodriguez-Valera F, Ventosa A. Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach. Front Microbiol 2014; 5:196. [PMID: 24847316 PMCID: PMC4021199 DOI: 10.3389/fmicb.2014.00196] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/12/2014] [Indexed: 12/02/2022] Open
Abstract
We analyzed the prokaryotic community structure of a saltern pond with 21% total salts located in Isla Cristina, Huelva, Southwest Spain, close to the Atlantic ocean coast. For this purpose, we constructed a metagenome (designated as IC21) obtained by pyrosequencing consisting of 486 Mb with an average read length of 397 bp and compared it with other metagenomic datasets obtained from ponds with 19, 33, and 37% total salts acquired from Santa Pola marine saltern, located in Alicante, East Spain, on the Mediterranean coast. Although the salinity in IC21 is closer to the pond with 19% total salts from Santa Pola saltern (designated as SS19), IC21 is more similar at higher taxonomic levels to the pond with 33% total salts from Santa Pola saltern (designated as SS33), since both are predominated by the phylum Euryarchaeota. However, there are significant differences at lower taxonomic levels where most sequences were related to the genus Halorubrum in IC21 and to Haloquadratum in SS33. Within the Bacteroidetes, the genus Psychroflexus is the most abundant in IC21 while Salinibacter dominates in SS33. Sequences related to bacteriorhodopsins and halorhodopsins correlate with the abundance of Haloquadratum in Santa Pola SS19 to SS33 and of Halorubrum in Isla Cristina IC21 dataset, respectively. Differences in composition might be attributed to local ecological conditions since IC21 showed a decrease in the number of sequences related to the synthesis of compatible solutes and in the utilization of phosphonate.
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Affiliation(s)
- Ana B Fernández
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
| | - Blanca Vera-Gargallo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
| | - Rohit Ghai
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante Alicante, Spain
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante Alicante, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
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Mallik S, Kundu S. Molecular interactions within the halophilic, thermophilic, and mesophilic prokaryotic ribosomal complexes: clues to environmental adaptation. J Biomol Struct Dyn 2014; 33:639-56. [PMID: 24697502 DOI: 10.1080/07391102.2014.900457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Using the available crystal structures of 50S ribosomal subunits from three prokaryotic species: Escherichia coli (mesophilic), Thermus thermophilus (thermophilic), and Haloarcula marismortui (halophilic), we have analyzed different structural features of ribosomal RNAs (rRNAs), proteins, and of their interfaces. We have correlated these structural features with the environmental adaptation strategies of the corresponding species. While dense intra-rRNA packing is observed in thermophilic, loose intra-rRNA packing is observed in halophilic (both compared to mesophilic). Interestingly, protein-rRNA interfaces of both the extremophiles are densely packed compared to that of the mesophilic. The intersubunit bridge regions are almost devoid of cavities, probably ensuring the proper formation of each bridge (by not allowing any loosely packed region nearby). During rRNA binding, the ribosomal proteins experience some structural transitions. Here, we have analyzed the intrinsically disordered and ordered regions of the ribosomal proteins, which are subjected to such transitions. The intrinsically disordered and disorder-to-order transition sites of the thermophilic and mesophilic ribosomal proteins are simultaneously (i) highly conserved and (ii) slowly evolving compared to rest of the protein structure. Although high conservation is observed at such sites of halophilic ribosomal proteins, but slow rate of evolution is absent. Such differences between thermophilic, mesophilic, and halophilic can be explained from their environmental adaptation strategy. Interestingly, a universal biophysical principle evident by a linear relationship between the free energy of interface formation, interface area, and structural changes of r-proteins during assembly is always maintained, irrespective of the environmental conditions.
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Affiliation(s)
- Saurav Mallik
- a Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, APC Road, Kolkata 700009 , India
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Zhang R, Zhang CT. A Brief Review: The Z-curve Theory and its Application in Genome Analysis. Curr Genomics 2014; 15:78-94. [PMID: 24822026 PMCID: PMC4009844 DOI: 10.2174/1389202915999140328162433] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 10/16/2013] [Accepted: 10/16/2013] [Indexed: 11/22/2022] Open
Abstract
In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.
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Affiliation(s)
- Ren Zhang
- Center for Molecular Medicine and Genetics, Wayne State University Medical School, Detroit, MI 48201, USA
| | - Chun-Ting Zhang
- Department of Physics, Tianjin University, Tianjin 300072, China
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Chimileski S, Dolas K, Naor A, Gophna U, Papke RT. Extracellular DNA metabolism in Haloferax volcanii. Front Microbiol 2014; 5:57. [PMID: 24600440 PMCID: PMC3929857 DOI: 10.3389/fmicb.2014.00057] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 01/29/2014] [Indexed: 11/29/2022] Open
Abstract
Extracellular DNA is found in all environments and is a dynamic component of the microbial ecosystem. Microbial cells produce and interact with extracellular DNA through many endogenous mechanisms. Extracellular DNA is processed and internalized for use as genetic information and as a major source of macronutrients, and plays several key roles within prokaryotic biofilms. Hypersaline sites contain some of the highest extracellular DNA concentrations measured in nature–a potential rich source of carbon, nitrogen, and phosphorus for halophilic microorganisms. We conducted DNA growth studies for the halophilic archaeon Haloferax volcanii DS2 and show that this model Halobacteriales strain is capable of using exogenous double-stranded DNA as a nutrient. Further experiments with varying medium composition, DNA concentration, and DNA types revealed that DNA is utilized primarily as a phosphorus source, that growth on DNA is concentration-dependent, and that DNA isolated from different sources is metabolized selectively, with a bias against highly divergent methylated DNA. Additionally, fluorescence microscopy showed that labeled DNA co-localized with H. volcanii cells. The gene Hvo_1477 was also identified using a comparative genomic approach as a factor likely to be involved in DNA processing at the cell surface, and deletion of Hvo_1477 created a strain deficient in the ability to grow on extracellular DNA. Widespread distribution of Hvo_1477 homologs in archaea suggests metabolism of extracellular DNA may be of broad ecological and physiological relevance in this domain of life.
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Affiliation(s)
- Scott Chimileski
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Kunal Dolas
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Adit Naor
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University Tel Aviv, Israel
| | - Uri Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University Tel Aviv, Israel
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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Affiliation(s)
- Joel A. Farkas
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Jonathan W. Picking
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Thomas J. Santangelo
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523;
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Protein adaptations in archaeal extremophiles. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:373275. [PMID: 24151449 PMCID: PMC3787623 DOI: 10.1155/2013/373275] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/26/2013] [Accepted: 08/14/2013] [Indexed: 12/25/2022]
Abstract
Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity under cold temperatures. Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity.
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Eichler J, Maupin-Furlow J. Post-translation modification in Archaea: lessons from Haloferax volcanii and other haloarchaea. FEMS Microbiol Rev 2012; 37:583-606. [PMID: 23167813 DOI: 10.1111/1574-6976.12012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 11/13/2012] [Accepted: 11/13/2012] [Indexed: 01/11/2023] Open
Abstract
As an ever-growing number of genome sequences appear, it is becoming increasingly clear that factors other than genome sequence impart complexity to the proteome. Of the various sources of proteomic variability, post-translational modifications (PTMs) most greatly serve to expand the variety of proteins found in the cell. Likewise, modulating the rates at which different proteins are degraded also results in a constantly changing cellular protein profile. While both strategies for generating proteomic diversity are adopted by organisms across evolution, the responsible pathways and enzymes in Archaea are often less well described than are their eukaryotic and bacterial counterparts. Studies on halophilic archaea, in particular Haloferax volcanii, originally isolated from the Dead Sea, are helping to fill the void. In this review, recent developments concerning PTMs and protein degradation in the haloarchaea are discussed.
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Affiliation(s)
- Jerry Eichler
- Department of Life Sciences, Ben Gurion University, Beersheva, Israel.
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Chen S, Tulloss RE, Liu Y, Feng B, Zhao Z, Yang ZL. Lateral gene transfer occurring in haloarchaea: an interpretative imitation study. World J Microbiol Biotechnol 2012; 28:2913-8. [PMID: 22806731 DOI: 10.1007/s11274-012-1101-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 06/06/2012] [Indexed: 11/26/2022]
Abstract
Lateral gene transfer (LGT) plays an important role in the molecular evolution of haloarchaea. Polyethylene glycol-mediated LGT in haloarchaea has been demonstrated in the laboratory, yet few explanations have been put forward for the apparently common, natural occurrence of plentiful plasmids within haloarchaeal cells. In this study, LGT was induced in two genera of haloarchaea, Haloferax and Halorubrum, by modification of salt concentration of media-a factor that may vary naturally in native haloarchaeal habitat. Minimal growth salt concentrations (MGSCs) of four strains of haloarchaea from these two genera were established, and transformations using two circular double-stranded DNAs (dsDNAs), pSY1 and pWL102, were then produced in media at strain-appropriate MGSCs. The four strains of haloarchaea were transformed successfully by both kinds of dsDNAs with an efficiency of 10(2)-10(3) transformants per microgram dsDNA. The transformation under reduced salt concentration may be an imitation of natural LGT of dsDNA into haloarchaea when salinity in normally hypersaline environments is altered by sudden introduction of fresh water--for example, by rainfall, snow-melt, or flooding--providing a reasonable interpretation for haloarchaea being naturally richer in plasmids than any other known organisms.
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Affiliation(s)
- Shaoxing Chen
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Cai L, Zhao D, Hou J, Wu J, Cai S, Dassarma P, Xiang H. Cellular and organellar membrane-associated proteins in haloarchaea: Perspectives on the physiological significance and biotechnological applications. SCIENCE CHINA-LIFE SCIENCES 2012; 55:404-14. [DOI: 10.1007/s11427-012-4321-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 04/15/2012] [Indexed: 11/24/2022]
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Siddaramappa S, Challacombe JF, DeCastro RE, Pfeiffer F, Sastre DE, Giménez MI, Paggi RA, Detter JC, Davenport KW, Goodwin LA, Kyrpides N, Tapia R, Pitluck S, Lucas S, Woyke T, Maupin-Furlow JA. A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. BMC Genomics 2012; 13:165. [PMID: 22559199 PMCID: PMC3403918 DOI: 10.1186/1471-2164-13-165] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 05/04/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Natrialba magadii is an aerobic chemoorganotrophic member of the Euryarchaeota and is a dual extremophile requiring alkaline conditions and hypersalinity for optimal growth. The genome sequence of Nab. magadii type strain ATCC 43099 was deciphered to obtain a comprehensive insight into the genetic content of this haloarchaeon and to understand the basis of some of the cellular functions necessary for its survival. RESULTS The genome of Nab. magadii consists of four replicons with a total sequence of 4,443,643 bp and encodes 4,212 putative proteins, some of which contain peptide repeats of various lengths. Comparative genome analyses facilitated the identification of genes encoding putative proteins involved in adaptation to hypersalinity, stress response, glycosylation, and polysaccharide biosynthesis. A proton-driven ATP synthase and a variety of putative cytochromes and other proteins supporting aerobic respiration and electron transfer were encoded by one or more of Nab. magadii replicons. The genome encodes a number of putative proteases/peptidases as well as protein secretion functions. Genes encoding putative transcriptional regulators, basal transcription factors, signal perception/transduction proteins, and chemotaxis/phototaxis proteins were abundant in the genome. Pathways for the biosynthesis of thiamine, riboflavin, heme, cobalamin, coenzyme F420 and other essential co-factors were deduced by in depth sequence analyses. However, approximately 36% of Nab. magadii protein coding genes could not be assigned a function based on Blast analysis and have been annotated as encoding hypothetical or conserved hypothetical proteins. Furthermore, despite extensive comparative genomic analyses, genes necessary for survival in alkaline conditions could not be identified in Nab. magadii. CONCLUSIONS Based on genomic analyses, Nab. magadii is predicted to be metabolically versatile and it could use different carbon and energy sources to sustain growth. Nab. magadii has the genetic potential to adapt to its milieu by intracellular accumulation of inorganic cations and/or neutral organic compounds. The identification of Nab. magadii genes involved in coenzyme biosynthesis is a necessary step toward further reconstruction of the metabolic pathways in halophilic archaea and other extremophiles. The knowledge gained from the genome sequence of this haloalkaliphilic archaeon is highly valuable in advancing the applications of extremophiles and their enzymes.
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Affiliation(s)
| | - Jean F Challacombe
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Rosana E DeCastro
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3250 4to Nivel, Mar del Plata, 7600, Argentina
| | - Friedhelm Pfeiffer
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany
| | - Diego E Sastre
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3250 4to Nivel, Mar del Plata, 7600, Argentina
| | - María I Giménez
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3250 4to Nivel, Mar del Plata, 7600, Argentina
| | - Roberto A Paggi
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3250 4to Nivel, Mar del Plata, 7600, Argentina
| | - John C Detter
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Karen W Davenport
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Lynne A Goodwin
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Samuel Pitluck
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Bldg. 981, Museum Rd., P.O. Box 110700, Gainesville, FL, 32611-0700, USA
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Ordóñez MV, Nercessian D, Conde RD. Nmag_2608, an extracellular ubiquitin-like domain-containing protein from the haloalkaliphilic archaeon Natrialba magadii. Extremophiles 2012; 16:437-46. [PMID: 22488573 DOI: 10.1007/s00792-012-0443-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/22/2012] [Indexed: 02/07/2023]
Abstract
Ubiquitin-like proteins (Ubls) and ubiquitin-like domain-containing proteins (Ulds) found in both eukaryotes and prokaryotes display an ubiquitin fold. We previously characterized a 124-amino acid polypeptide (P400) from the haloalkaliphilic archaeon Natrialba magadii having structural homology with ubiquitin family proteins. The reported N. magadii's genome allowed the identification of the Nmag_2608 gene for the protein containing P400, which belongs to specific orthologs of halophilic organisms. It was found that Nmag_2608 has an N-terminal signal peptide with a lipobox motif characteristic of bacterial lipoproteins. Also, it presents partial identity with the ubiquitin-like domain-containing proteins, soluble ligand binding β-grasp proteins. Western blots and heterologous expression tests in E. coli evidenced that Nmag_2608 is processed and secreted outside the cell, where it could perform its function. The analysis of Nmag_2608 expression in N. magadii's cells suggests a co-transcription with the adjoining Nmag_2609 gene encoding a protein of the cyclase family. Also, the transcript level decreased in cells grown in low salinity and starved. To conclude, this work reports for the first time an extracellular archaeal protein with an ubiquitin-like domain.
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Affiliation(s)
- María Victoria Ordóñez
- Degradación de Proteínas, Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CONICET, Funes 3250 CC 1245, 7600, Mar del Plata, Argentina.
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