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Molecular Biology of Extremophiles
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Molecular Biology of Extremophiles

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 April 2021) | Viewed by 23479

Special Issue Editors

Prof. Dr. María José Bonete

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Guest Editor
Department of Agrochemistry and Biochemistry, Universitat d'Alacant, E-03080 Alicante, Spain
Interests: extremophiles; haloarchaea; nitrogen metabolism; stress response; bioremediation
Special Issues, Collections and Topics in MDPI journals
Dr. Mónica Camacho

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Guest Editor
Department of Agrochemistry and Biochemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, E-03080 Alicante, Spain
Interests: genomics; proteomics; extremophiles; systems biology; protein expression and characterization; protein-protein interactions
Special Issues, Collections and Topics in MDPI journals
Dr. Julia Esclapez

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Guest Editor
Department of Agrochemistry and Biochemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
Interests: archaea; molecular biology; stress response; proteins; small RNAs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Extremophilic organisms are widespread in the three domains of life. It is known that they play a key role in several environments since they are major contributors to biogeochemical cycles (nitrogen, carbon, iron, sulphur, etc.). Over recent years, most research has focused on these species which resist under stress conditions (temperature, salinity, pH, etc.) at the limits of sustainable life, enabled by efficient stress-repair systems and unique metabolic capabilities. These biological characteristics along with the adaptation mechanism developed for their molecular machinery may represent a great economic potential in many industrial processes, including environmental applications in food, agriculture, and pharmacy, among others. However, limited knowledge about these organisms results in a bottleneck that makes their use as microbial factories for industrial applications difficult.

Knowledge about extremophilic organisms has advanced over recent years thanks to the development of high performance genetic tools and techniques. However, there is still a long way to go in this sense.

This Special Issue welcomes submissions related to molecular biology studies focused on extremophilic microorganisms, covering aspects of their metabolism and gene expression, such as transcriptional and translational regulation, DNA–protein or protein–protein interaction, overexpression of proteins as well as their biotechnological application.

Prof. Dr. María José Bonete
Prof. Dr. Mónica Camacho
Dr. Julia Esclapez
Guest Editors

Manuscript Submission Information

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Keywords

  • Extremophiles
  • Archaea
  • Regulation of metabolism pathways
  • Gene regulation networks
  • DNA-protein and protein-protein interactions
  • Stress responses
  • OMICS (Genomics, Transcriptomics, Proteomics, Metabolomics)
  • Biotechnological applications

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Published Papers (7 papers)

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19 pages, 2907 KiB  
Article
Halobacterium salinarum and Haloferax volcanii Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites
by Amr Galal Abd El-Raheem Ibrahim, Ricardo Z. N. Vêncio, Alan P. R. Lorenzetti and Tie Koide
Genes 2021, 12(7), 1018; https://doi.org/10.3390/genes12071018 - 30 Jun 2021
Cited by 3 | Viewed by 2943
Abstract
Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e., ribonucleases which implement the cleavages) is generally more studied than the RNA [...] Read more.
Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e., ribonucleases which implement the cleavages) is generally more studied than the RNA perspective (i.e., processing sites). In the present in silico work, we mapped genome-wide transcriptional processing sites (TPS) in two halophilic model organisms, Halobacterium salinarum NRC-1 and Haloferax volcanii DS2. TPS were established by reanalysis of publicly available differential RNA-seq (dRNA-seq) data, searching for non-primary (monophosphorylated RNAs) enrichment. We found 2093 TPS in 43% of H. salinarum genes and 3515 TPS in 49% of H. volcanii chromosomal genes. Of the 244 conserved TPS sites found, the majority were located around start and stop codons of orthologous genes. Specific genes are highlighted when discussing antisense, ribosome and insertion sequence associated TPS. Examples include the cell division gene ftsZ2, whose differential processing signal along growth was detected and correlated with post-transcriptional regulation, and biogenesis of sense overlapping transcripts associated with IS200/IS605. We hereby present the comparative, transcriptomics-based processing site maps with a companion browsing interface. Full article
(This article belongs to the Special Issue Molecular Biology of Extremophiles)
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43 pages, 1738 KiB  
Article
Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
by Friedhelm Pfeiffer and Mike Dyall-Smith
Genes 2021, 12(7), 963; https://doi.org/10.3390/genes12070963 - 24 Jun 2021
Cited by 3 | Viewed by 3324
Abstract
Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very [...] Read more.
Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions. Full article
(This article belongs to the Special Issue Molecular Biology of Extremophiles)
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17 pages, 2877 KiB  
Article
Analysis of Haloferax mediterranei Lrp Transcriptional Regulator
by Laura Matarredona, Mónica Camacho, María-José García-Bonete, Belén Esquerra, Basilio Zafrilla, Julia Esclapez and María-José Bonete
Genes 2021, 12(6), 802; https://doi.org/10.3390/genes12060802 - 25 May 2021
Cited by 9 | Viewed by 3828
Abstract
Haloferax mediterranei is an extremely halophilic archaeon, able to live in hypersaline environments with versatile nutritional requirements, whose study represents an excellent basis in the field of biotechnology. The transcriptional machinery in Archaea combines the eukaryotic basal apparatus and the bacterial regulation mechanisms. [...] Read more.
Haloferax mediterranei is an extremely halophilic archaeon, able to live in hypersaline environments with versatile nutritional requirements, whose study represents an excellent basis in the field of biotechnology. The transcriptional machinery in Archaea combines the eukaryotic basal apparatus and the bacterial regulation mechanisms. However, little is known about molecular mechanisms of gene expression regulation compared with Bacteria, particularly in Haloarchaea. The genome of Hfx. mediterranei contains a gene, lrp (HFX_RS01210), which encodes a transcriptional factor belonging to Lrp/AsnC family. It is located downstream of the glutamine synthetase gene (HFX_RS01205), an enzyme involved in ammonium assimilation and amino acid metabolism. To study this transcriptional factor more deeply, the lrp gene has been homologously overexpressed and purified under native conditions by two chromatographic steps, namely nickel affinity and gel filtration chromatography, showing that Lrp behaves asa tetrameric protein of approximately 67 kDa. Its promoter region has been characterized under different growth conditions using bgaH as a reporter gene. The amount of Lrp protein was also analyzed by Western blotting in different nitrogen sources and under various stress conditions. To sum up, regarding its involvement in the nitrogen cycle, it has been shown that its expression profile does not change in response to the nitrogen sources tested. Differences in its expression pattern have been observed under different stress conditions, such as in the presence of hydrogen peroxide or heavy metals. According to these results, the Lrp seems to be involved in a general response against stress factors, acting as a first-line transcriptional regulator. Full article
(This article belongs to the Special Issue Molecular Biology of Extremophiles)
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14 pages, 2377 KiB  
Article
Towards the Elucidation of Assimilative nasABC Operon Transcriptional Regulation in Haloferax mediterranei
by Sandra Pastor-Soler, Mónica Camacho, Vanesa Bautista, María-José Bonete and Julia Esclapez
Genes 2021, 12(5), 619; https://doi.org/10.3390/genes12050619 - 22 Apr 2021
Cited by 8 | Viewed by 2234
Abstract
The assimilatory pathway of the nitrogen cycle in the haloarchaeon Haloferax mediterranei has been well described and characterized in previous studies. However, the regulatory mechanisms involved in the gene expression of this pathway remain unknown in haloarchaea. This work focuses on elucidating the [...] Read more.
The assimilatory pathway of the nitrogen cycle in the haloarchaeon Haloferax mediterranei has been well described and characterized in previous studies. However, the regulatory mechanisms involved in the gene expression of this pathway remain unknown in haloarchaea. This work focuses on elucidating the regulation at the transcriptional level of the assimilative nasABC operon (HFX_2002 to HFX_2004) through different approaches. Characterization of its promoter region using β-galactosidase as a reporter gene and site-directed mutagenesis has allowed us to identify possible candidate binding regions for a transcriptional factor. The identification of a potential transcriptional regulator related to nitrogen metabolism has become a real challenge due to the lack of information on haloarchaea. The investigation of protein–DNA binding by streptavidin bead pull-down analysis combined with mass spectrometry resulted in the in vitro identification of a transcriptional regulator belonging to the Lrp/AsnC family, which binds to the nasABC operon promoter (p.nasABC). To our knowledge, this study is the first report to suggest the AsnC transcriptional regulator as a powerful candidate to play a regulatory role in nasABC gene expression in Hfx. mediterranei and, in general, in the assimilatory nitrogen pathway. Full article
(This article belongs to the Special Issue Molecular Biology of Extremophiles)
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12 pages, 2150 KiB  
Article
Quorum Sensing Signaling Molecules Positively Regulate c-di-GMP Effector PelD Encoding Gene and PEL Exopolysaccharide Biosynthesis in Extremophile Bacterium Acidithiobacillus thiooxidans
by Mauricio Díaz, Diego San Martin, Matías Castro, Mario Vera and Nicolás Guiliani
Genes 2021, 12(1), 69; https://doi.org/10.3390/genes12010069 - 7 Jan 2021
Cited by 11 | Viewed by 3338
Abstract
Acidithiobacillus species are fundamental players in biofilm formation by acidophile bioleaching communities. It has been previously reported that Acidithiobacillus ferrooxidans possesses a functional quorum sensing mediated by acyl-homoserine lactones (AHL), involved in biofilm formation, and AHLs naturally produced by Acidithiobacillus species also induce [...] Read more.
Acidithiobacillus species are fundamental players in biofilm formation by acidophile bioleaching communities. It has been previously reported that Acidithiobacillus ferrooxidans possesses a functional quorum sensing mediated by acyl-homoserine lactones (AHL), involved in biofilm formation, and AHLs naturally produced by Acidithiobacillus species also induce biofilm formation in Acidithiobacillus thiooxidans. A c-di-GMP pathway has been characterized in Acidithiobacillus species but it has been pointed out that the c-di-GMP effector PelD and pel-like operon are only present in the sulfur oxidizers such as A. thiooxidans. PEL exopolysaccharide has been recently involved in biofilm formation in this Acidithiobacillus species. Here, by comparing wild type and ΔpelD strains through mechanical analysis of biofilm-cells detachment, fluorescence microscopy and qPCR experiments, the structural role of PEL exopolysaccharide and the molecular network involved for its biosynthesis by A. thiooxidans were tackled. Besides, the effect of AHLs on PEL exopolysaccharide production was assessed. Mechanical resistance experiments indicated that the loss of PEL exopolysaccharide produces fragile A. thiooxidans biofilms. qRT-PCR analysis established that AHLs induce the transcription of pelA and pelD genes while epifluorescence microscopy studies revealed that PEL exopolysaccharide was required for the development of AHL-induced biofilms. Altogether these results reveal for the first time that AHLs positively regulate pel genes and participate in the molecular network for PEL exopolysaccharide biosynthesis by A. thiooxidans. Full article
(This article belongs to the Special Issue Molecular Biology of Extremophiles)
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12 pages, 1979 KiB  
Article
Mutations Affecting HVO_1357 or HVO_2248 Cause Hypermotility in Haloferax volcanii, Suggesting Roles in Motility Regulation
by Michiyah Collins, Simisola Afolayan, Aime B. Igiraneza, Heather Schiller, Elise Krespan, Daniel P. Beiting, Mike Dyall-Smith, Friedhelm Pfeiffer and Mechthild Pohlschroder
Genes 2021, 12(1), 58; https://doi.org/10.3390/genes12010058 - 31 Dec 2020
Cited by 7 | Viewed by 3879
Abstract
Motility regulation plays a key role in prokaryotic responses to environmental stimuli. Here, we used a motility screen and selection to isolate hypermotile Haloferax volcanii mutants from a transposon insertion library. Whole genome sequencing revealed that hypermotile mutants were predominantly affected in two [...] Read more.
Motility regulation plays a key role in prokaryotic responses to environmental stimuli. Here, we used a motility screen and selection to isolate hypermotile Haloferax volcanii mutants from a transposon insertion library. Whole genome sequencing revealed that hypermotile mutants were predominantly affected in two genes that encode HVO_1357 and HVO_2248. Alterations of these genes comprised not only transposon insertions but also secondary genome alterations. HVO_1357 contains a domain that was previously identified in the regulation of bacteriorhodopsin transcription, as well as other domains frequently found in two-component regulatory systems. The genes adjacent to hvo_1357 encode a sensor box histidine kinase and a response regulator, key players of a two-component regulatory system. None of the homologues of HVO_2248 have been characterized, nor does it contain any of the assigned InterPro domains. However, in a significant number of Haloferax species, the adjacent gene codes for a chemotaxis receptor/transducer. Our results provide a foundation for characterizing the root causes underlying Hfx. volcanii hypermotility. Full article
(This article belongs to the Special Issue Molecular Biology of Extremophiles)
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16 pages, 2186 KiB  
Review
Nitrate Respiration in Thermus thermophilus NAR1: from Horizontal Gene Transfer to Internal Evolution
by Mercedes Sánchez-Costa, Alba Blesa and José Berenguer
Genes 2020, 11(11), 1308; https://doi.org/10.3390/genes11111308 - 4 Nov 2020
Cited by 6 | Viewed by 2786
Abstract
Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus Thermus, but only in few strains of the species Thermus thermophilus has the pathway been studied to a certain detail. Here, we review the enzymes [...] Read more.
Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus Thermus, but only in few strains of the species Thermus thermophilus has the pathway been studied to a certain detail. Here, we review the enzymes involved in this pathway present in T. thermophilus NAR1, a strain extensively employed as a model for nitrate respiration, in the light of its full sequence recently assembled through a combination of PacBio and Illumina technologies in order to counteract the systematic errors introduced by the former technique. The genome of this strain is divided in four replicons, a chromosome of 2,021,843 bp, two megaplasmids of 370,865 and 77,135 bp and a small plasmid of 9799 pb. Nitrate respiration is encoded in the largest megaplasmid, pTTHNP4, within a region that includes operons for O2 and nitrate sensory systems, a nitrate reductase, nitrate and nitrite transporters and a nitrate specific NADH dehydrogenase, in addition to multiple insertion sequences (IS), suggesting its mobility-prone nature. Despite nitrite is the final product of nitrate respiration in this strain, the megaplasmid encodes two putative nitrite reductases of the cd1 and Cu-containing types, apparently inactivated by IS. No nitric oxide reductase genes have been found within this region, although the NorR sensory gene, needed for its expression, is found near the inactive nitrite respiration system. These data clearly support that partial denitrification in this strain is the consequence of recent deletions and IS insertions in genes involved in nitrite respiration. Based on these data, the capability of this strain to transfer or acquire denitrification clusters by horizontal gene transfer is discussed. Full article
(This article belongs to the Special Issue Molecular Biology of Extremophiles)
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