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Pal N, Sinha S, Shivani, Chakraborty M. A review on bacterial and archaeal thermostable sulfur oxidoreductases (SORS)-an insight into the biochemical, molecular and in-silico structural comparative analysis of a neglected thermostable enzyme of industrial significance. Arch Microbiol 2022; 204:655. [PMID: 36175582 DOI: 10.1007/s00203-022-03256-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/02/2022]
Abstract
Diverse thermophilic microorganisms with the potential to withstand extreme physiological conditions have long been investigated and explored for human commercial benefit. Thermozymes with distinct functional and structural properties isolated from these thermophiles are known to have high thermostability without significant loss of specific enzyme activity. Thermophiles isolated and characterised from the thermophilic ecological niche of India are well documented. There is a plethora of work in the literature emphasising its industrial significance. However, in-depth knowledge of the thermophilic oxidoreductase group of enzymes (Oxizymes) is restricted. Sulfur Oxygenase Reductases or Sulfur Oxygen-Reductases (SORs) are a group of thermophilic oxizymes reported predominantly from thermophilic and mesophilic archaea and bacteria, which catalyse oxygen-dependent disproportionation reactions of elemental sulfur, producing sulfite, thiosulfate, and sulphide. There have been few reports on isolated and characterised SORs from the Indian geothermal niche. The review article will highlight the SORs reported till date with a concise overview of different archaeal and bacterial species producing the enzymes. Based on the literature available till date, characteristics including physico-chemical properties, amino acid sequence homology, conserved motifs and their 3D structure comparison have been discussed. In-silico sequence and structure level preliminary comparative analysis of various SORs has also been discussed. However, a few SORs whose structural information is not reported in the protein data bank have been modelled to enrich our analysis.
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Affiliation(s)
- Nirmalya Pal
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Sanjana Sinha
- NMR Micro-Imaging and Spectroscopy Laboratory, Centre for Cellular and Molecular Biology, Uppal Rd, IICT Colony, Habsiguda, Hyderabad, 500007, Telangana, India
| | - Shivani
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Mitun Chakraborty
- Department of Biotechnology Engineering and Food Technology, University Institute of Engineering, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India.
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2
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Thakur N, Sharma N, Kumar V, Bhalla TC. Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190718150627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Amidases are ubiquitous enzymes and biological functions of these enzymes
vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of
carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals
synthesis, pharmaceuticals agrochemicals and wastewater treatments.
Methods:
They hydrolyse a wide variety of amides (short-chain aliphatic amides, mid-chain amides,
arylamides, α-aminoamides and α-hydroxyamides) and can be grouped on the basis of their catalytic
site and preferred substrate. Despite their economic importance, we lack knowledge as to how these
amidases withstand elevated pH and temperature whereas others cannot.
Results:
The present study focuses on the statistical comparison between the acid-tolerant, alkali tolerant
and neutrophilic organisms. In silico analysis of amidases of acid-tolerant, alkali tolerant and neutrophilic
organisms revealed some striking trends as to how amino acid composition varies significantly.
Statistical analysis of primary and secondary structure revealed amino acid trends in amidases of
these three groups of bacteria. The abundance of isoleucine (Ile, I) in acid-tolerant and leucine (Leu, L)
in alkali tolerant showed the aliphatic amino acid dominance in extreme conditions of pH in acidtolerant
and alkali tolerant amidases.
Conclusion:
The present investigation insights physiochemical properties and dominance of some crucial
amino acid residues in the primary and secondary structure of some amidases from acid-tolerant,
alkali tolerant and neutrophilic microorganisms.
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Affiliation(s)
- Neerja Thakur
- Bioinformatics Centre, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Nikhil Sharma
- Bioinformatics Centre, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Vijay Kumar
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Tek Chand Bhalla
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
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3
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Panyushkina AE, Babenko VV, Nikitina AS, Selezneva OV, Tsaplina IA, Letarova MA, Kostryukova ES, Letarov AV. Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs. Sci Rep 2019; 9:15069. [PMID: 31636299 PMCID: PMC6803676 DOI: 10.1038/s41598-019-51486-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 09/23/2019] [Indexed: 11/09/2022] Open
Abstract
The first complete genome of the biotechnologically important species Sulfobacillus thermotolerans has been sequenced. Its 3 317 203-bp chromosome contains an 83 269-bp plasmid-like region, which carries heavy metal resistance determinants and the rusticyanin gene. Plasmid-mediated metal resistance is unusual for acidophilic chemolithotrophs. Moreover, most of their plasmids are cryptic and do not contribute to the phenotype of the host cells. A polyphosphate-based mechanism of metal resistance, which has been previously unknown in the genus Sulfobacillus or other Gram-positive chemolithotrophs, potentially operates in two Sulfobacillus species. The methylcitrate cycle typical for pathogens and identified in the genus Sulfobacillus for the first time can fulfill the energy and/or protective function in S. thermotolerans Kr1 and two other Sulfobacillus species, which have incomplete glyoxylate cycles. It is notable that the TCA cycle, disrupted in all Sulfobacillus isolates under optimal growth conditions, proved to be complete in the cells enduring temperature stress. An efficient antioxidant defense system gives S. thermotolerans another competitive advantage in the microbial communities inhabiting acidic metal-rich environments. The genomic comparisons revealed 80 unique genes in the strain Kr1, including those involved in lactose/galactose catabolism. The results provide new insights into metabolism and resistance mechanisms in the Sulfobacillus genus and other acidophiles.
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Affiliation(s)
- Anna E Panyushkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia.
| | - Vladislav V Babenko
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Anastasia S Nikitina
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Oksana V Selezneva
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Iraida A Tsaplina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Maria A Letarova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Elena S Kostryukova
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Andrey V Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
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4
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Kadnikov VV, Gruzdev EV, Ivasenko DA, Beletsky AV, Mardanov AV, Danilova EV, Karnachuk OV, Ravin NV. Selection of a Microbial Community in the Course of Formation of Acid Mine Drainage. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719030056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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5
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Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies. MINERALS 2018. [DOI: 10.3390/min8120596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.
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Hart A, Cortés MP, Latorre M, Martinez S. Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium. PLoS One 2018; 13:e0195869. [PMID: 29742107 PMCID: PMC5942774 DOI: 10.1371/journal.pone.0195869] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/30/2018] [Indexed: 11/20/2022] Open
Abstract
The analysis of codon usage bias has been widely used to characterize different communities of microorganisms. In this context, the aim of this work was to study the codon usage bias in a natural consortium of five acidophilic bacteria used for biomining. The codon usage bias of the consortium was contrasted with genes from an alternative collection of acidophilic reference strains and metagenome samples. Results indicate that acidophilic bacteria preferentially have low codon usage bias, consistent with both their capacity to live in a wide range of habitats and their slow growth rate, a characteristic probably acquired independently from their phylogenetic relationships. In addition, the analysis showed significant differences in the unique sets of genes from the autotrophic species of the consortium in relation to other acidophilic organisms, principally in genes which code for proteins involved in metal and oxidative stress resistance. The lower values of codon usage bias obtained in this unique set of genes suggest higher transcriptional adaptation to living in extreme conditions, which was probably acquired as a measure for resisting the elevated metal conditions present in the mine.
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Affiliation(s)
- Andrew Hart
- UMI 2071 CNRS-UCHILE, Facultad de Ciencias Físicas y Matemáticas, Centro de Modelamiento Matemático, Universidad de Chile, Casilla 170, Correo 3, Santiago, Chile
| | - María Paz Cortés
- Mathomics, Centro de Modelamiento Matemático, Universidad de Chile, Santiago, Chile
- Fondap-Center of Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Mathomics, Centro de Modelamiento Matemático, Universidad de Chile, Santiago, Chile
- Fondap-Center of Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Macul, Santiago, Chile
- Universidad de O'Higgins, Instituto de Ciencias de la Ingeniería, Rancagua, Chile
- * E-mail: (ML); (SM)
| | - Servet Martinez
- Departamento de Ingeniería Matemática, UMI 2071 CNRS-UCHILE, Facultad de Ciencias Físicas y Matemáticas, Centro de Modelamiento Matemático, Universidad de Chile, Casilla 170, Correo 3, Santiago, Chile
- * E-mail: (ML); (SM)
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7
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Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss. Appl Environ Microbiol 2017; 83:AEM.03098-16. [PMID: 28115381 DOI: 10.1128/aem.03098-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/13/2017] [Indexed: 12/27/2022] Open
Abstract
Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with Sulfobacillusthermosulfidooxidans Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the Sulfobacillus genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The Sulfobacillus strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of Sulfobacillus strains.IMPORTANCE Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.
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8
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Cárdenas JP, Quatrini R, Holmes DS. Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review. Res Microbiol 2016; 167:529-38. [PMID: 27394987 DOI: 10.1016/j.resmic.2016.06.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 12/19/2022]
Abstract
High-throughput genomic technologies are accelerating progress in understanding the diversity of microbial life in many environments. Here we highlight advances in genomics and metagenomics of microorganisms from bioleaching heaps and related acidic mining environments. Bioleaching heaps used for copper recovery provide significant opportunities to study the processes and mechanisms underlying microbial successions and the influence of community composition on ecosystem functioning. Obtaining quantitative and process-level knowledge of these dynamics is pivotal for understanding how microorganisms contribute to the solubilization of copper for industrial recovery. Advances in DNA sequencing technology provide unprecedented opportunities to obtain information about the genomes of bioleaching microorganisms, allowing predictive models of metabolic potential and ecosystem-level interactions to be constructed. These approaches are enabling predictive phenotyping of organisms many of which are recalcitrant to genetic approaches or are unculturable. This mini-review describes current bioleaching genomic and metagenomic projects and addresses the use of genome information to: (i) build metabolic models; (ii) predict microbial interactions; (iii) estimate genetic diversity; and (iv) study microbial evolution. Key challenges and perspectives of bioleaching genomics/metagenomics are addressed.
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Affiliation(s)
| | | | - David S Holmes
- Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.
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9
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Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms. Appl Microbiol Biotechnol 2016; 100:6871-6880. [DOI: 10.1007/s00253-016-7537-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 03/29/2016] [Accepted: 04/05/2016] [Indexed: 11/26/2022]
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10
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Chen LX, Huang LN, Méndez-García C, Kuang JL, Hua ZS, Liu J, Shu WS. Microbial communities, processes and functions in acid mine drainage ecosystems. Curr Opin Biotechnol 2016; 38:150-8. [DOI: 10.1016/j.copbio.2016.01.013] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 10/22/2022]
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Sulfur Oxygenase Reductase (Sor) in the Moderately Thermoacidophilic Leaching Bacteria: Studies in Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus. Microorganisms 2015; 3:707-24. [PMID: 27682113 PMCID: PMC5023260 DOI: 10.3390/microorganisms3040707] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 10/01/2015] [Accepted: 10/10/2015] [Indexed: 12/15/2022] Open
Abstract
The sulfur oxygenase reductase (Sor) catalyzes the oxygen dependent disproportionation of elemental sulfur, producing sulfite, thiosulfate and sulfide. Being considered an “archaeal like” enzyme, it is also encoded in the genomes of some acidophilic leaching bacteria such as Acidithiobacillus caldus, Acidithiobacillus thiooxidans, Acidithiobacillus ferrivorans and Sulfobacillus thermosulfidooxidans, among others. We measured Sor activity in crude extracts from Sb. thermosulfidooxidans DSM 9293T. The optimum temperature for its oxygenase activity was achieved at 75 °C, confirming the “thermophilic” nature of this enzyme. Additionally, a search for genes probably involved in sulfur metabolism in the genome sequence of Sb. thermosulfidooxidans DSM 9293T was done. Interestingly, no sox genes were found. Two sor genes, a complete heterodisulfidereductase (hdr) gene cluster, three tetrathionate hydrolase (tth) genes, three sulfide quinonereductase (sqr), as well as the doxD component of a thiosulfate quinonereductase (tqo) were found. Seven At. caldus strains were tested for Sor activity, which was not detected in any of them. We provide evidence that an earlier reported Sor activity from At. caldus S1 and S2 strains most likely was due to the presence of a Sulfobacillus contaminant.
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Abstract
Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.
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Méndez-García C, Peláez AI, Mesa V, Sánchez J, Golyshina OV, Ferrer M. Microbial diversity and metabolic networks in acid mine drainage habitats. Front Microbiol 2015; 6:475. [PMID: 26074887 PMCID: PMC4448039 DOI: 10.3389/fmicb.2015.00475] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/29/2015] [Indexed: 11/13/2022] Open
Abstract
Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.
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Affiliation(s)
| | - Ana I. Peláez
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | - Victoria Mesa
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | - Jesús Sánchez
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | | | - Manuel Ferrer
- Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas, Institute of CatalysisMadrid, Spain
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14
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Fei L, Tian S, Moysey R, Misca M, Barker JJ, Smith MA, McEwan PA, Pilka ES, Crawley L, Evans T, Sun D. Structural and biochemical studies of a moderately thermophilic exonuclease I from Methylocaldum szegediense. PLoS One 2015; 10:e0117470. [PMID: 25658953 PMCID: PMC4319927 DOI: 10.1371/journal.pone.0117470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/25/2014] [Indexed: 11/18/2022] Open
Abstract
A novel exonuclease, designated as MszExo I, was cloned from Methylocaldum szegediense, a moderately thermophilic methanotroph. It specifically digests single-stranded DNA in the 3ʹ to 5ʹ direction. The protein is composed of 479 amino acids, and it shares 47% sequence identity with E. coli Exo I. The crystal structure of MszExo I was determined to a resolution of 2.2 Å and it aligns well with that of E. coli Exo I. Comparative studies revealed that MszExo I and E. coli Exo I have similar metal ion binding affinity and similar activity at mesophilic temperatures (25–47°C). However, the optimum working temperature of MszExo I is 10°C higher, and the melting temperature is more than 4°C higher as evaluated by both thermal inactivation assays and DSC measurements. More importantly, two thermal transitions during unfolding of MszExo I were monitored by DSC while only one transition was found in E. coli Exo I. Further analyses showed that magnesium ions not only confer structural stability, but also affect the unfolding of MszExo I. MszExo I is the first reported enzyme in the DNA repair systems of moderately thermophilic bacteria, which are predicted to have more efficient DNA repair systems than mesophilic ones.
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Affiliation(s)
- Li Fei
- New England Biolabs Shanghai R&D Center, Building 5, 917 Halei Road, Pudong District, Shanghai, China
| | - SiSi Tian
- New England Biolabs Shanghai R&D Center, Building 5, 917 Halei Road, Pudong District, Shanghai, China
| | - Ruth Moysey
- Oxford Nanopore Technologies Ltd., Edmund Cartwright House, 4 Robert Robinson Avenue Oxford Science Park, Oxford OX4, United Kingdom
| | - Mihaela Misca
- Oxford Nanopore Technologies Ltd., Edmund Cartwright House, 4 Robert Robinson Avenue Oxford Science Park, Oxford OX4, United Kingdom
| | - John J. Barker
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Myron A. Smith
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Paul A. McEwan
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Ewa S. Pilka
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Lauren Crawley
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Tom Evans
- New England Biolabs, 240 County Road, Ipswich, MA 01938–2723, United States of America
| | - Dapeng Sun
- New England Biolabs Shanghai R&D Center, Building 5, 917 Halei Road, Pudong District, Shanghai, China
- * E-mail:
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15
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Justice NB, Norman A, Brown CT, Singh A, Thomas BC, Banfield JF. Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics 2014; 15:1107. [PMID: 25511286 PMCID: PMC4378227 DOI: 10.1186/1471-2164-15-1107] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/27/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these environments, their role in biogeochemical cycling is poorly understood. RESULTS Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans. We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of nickel-iron hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate dehydrogenase complexes. CONCLUSIONS Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.
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Affiliation(s)
- Nicholas B Justice
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
- />Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA USA
| | - Anders Norman
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
- />Section for Infection Microbiology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christopher T Brown
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Andrea Singh
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Brian C Thomas
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Jillian F Banfield
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
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