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Reshma SV, Sathyanarayanan N, Nagendra HG. Characterization of hypothetical protein VNG0128C from Halobacterium NRC-1 reveals GALE like activity and its involvement in Leloir pathway of galactose metabolism. J Biomol Struct Dyn 2014; 33:1743-55. [PMID: 25397923 DOI: 10.1080/07391102.2014.969313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
VNG0128C, a hypothetical protein from Halobacterium NRC-1, was chosen for detailed insilico and experimental investigations. Computational exercises revealed that VNG0128C functions as NAD(+) binding protein. The phylogenetic analysis with the homolog sequences of VNG0128C suggested that it could act as UDP-galactose 4-epimerase. Hence, the VNG0128C sequence was modeled using a suitable template and docking studies were performed with NAD and UDP-galactose as ligands. The binding interactions strongly indicate that VNG0128C could plausibly act as UDP-galactose 4-epimerase. In order to validate these insilico results, VNG0128C was cloned in pUC57, subcloned in pET22b(+), expressed in BL21 cells and purified using nickel affinity chromatography. An assay using blue dextran was performed to confirm the presence of NAD binding domain. To corroborate the epimerase like enzymatic role of the hypothetical protein, i.e. the ability of the enzyme to convert UDP-galactose to UDP-glucose, the conversion of NAD to NADH was measured. The experimental assay significantly correlated with the insilico predictions, indicating that VNG0128C has a NAD(+) binding domain with epimerase activity. Consequently, its key role in nucleotide-sugar metabolism was thus established. Additionally, the work highlights the need for a methodical characterization of hypothetical proteins (less studied class of biopolymers) to exploit them for relevant applications in the field of biology.
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Affiliation(s)
- S V Reshma
- a Department of Biotechnology , PES Institute of Technology , Bangalore , India
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Madsen JA, Xu H, Robinson MR, Horton AP, Shaw JB, Giles DK, Kaoud TS, Dalby KN, Trent MS, Brodbelt JS. High-throughput database search and large-scale negative polarity liquid chromatography-tandem mass spectrometry with ultraviolet photodissociation for complex proteomic samples. Mol Cell Proteomics 2013; 12:2604-14. [PMID: 23695934 DOI: 10.1074/mcp.o113.028258] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The use of ultraviolet photodissociation (UVPD) for the activation and dissociation of peptide anions is evaluated for broader coverage of the proteome. To facilitate interpretation and assignment of the resulting UVPD mass spectra of peptide anions, the MassMatrix database search algorithm was modified to allow automated analysis of negative polarity MS/MS spectra. The new UVPD algorithms were developed based on the MassMatrix database search engine by adding specific fragmentation pathways for UVPD. The new UVPD fragmentation pathways in MassMatrix were rigorously and statistically optimized using two large data sets with high mass accuracy and high mass resolution for both MS(1) and MS(2) data acquired on an Orbitrap mass spectrometer for complex Halobacterium and HeLa proteome samples. Negative mode UVPD led to the identification of 3663 and 2350 peptides for the Halo and HeLa tryptic digests, respectively, corresponding to 655 and 645 peptides that were unique when compared with electron transfer dissociation (ETD), higher energy collision-induced dissociation, and collision-induced dissociation results for the same digests analyzed in the positive mode. In sum, 805 and 619 proteins were identified via UVPD for the Halobacterium and HeLa samples, respectively, with 49 and 50 unique proteins identified in contrast to the more conventional MS/MS methods. The algorithm also features automated charge determination for low mass accuracy data, precursor filtering (including intact charge-reduced peaks), and the ability to combine both positive and negative MS/MS spectra into a single search, and it is freely open to the public. The accuracy and specificity of the MassMatrix UVPD search algorithm was also assessed for low resolution, low mass accuracy data on a linear ion trap. Analysis of a known mixture of three mitogen-activated kinases yielded similar sequence coverage percentages for UVPD of peptide anions versus conventional collision-induced dissociation of peptide cations, and when these methods were combined into a single search, an increase of up to 13% sequence coverage was observed for the kinases. The ability to sequence peptide anions and cations in alternating scans in the same chromatographic run was also demonstrated. Because ETD has a significant bias toward identifying highly basic peptides, negative UVPD was used to improve the identification of the more acidic peptides in conjunction with positive ETD for the more basic species. In this case, tryptic peptides from the cytosolic section of HeLa cells were analyzed by polarity switching nanoLC-MS/MS utilizing ETD for cation sequencing and UVPD for anion sequencing. Relative to searching using ETD alone, positive/negative polarity switching significantly improved sequence coverages across identified proteins, resulting in a 33% increase in unique peptide identifications and more than twice the number of peptide spectral matches.
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Affiliation(s)
- James A Madsen
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, USA
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Liao WC, Ng WV, Lin IH, Syu WJ, Liu TT, Chang CH. T4-Like genome organization of the Escherichia coli O157:H7 lytic phage AR1. J Virol 2011; 85:6567-78. [PMID: 21507986 PMCID: PMC3126482 DOI: 10.1128/jvi.02378-10] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 04/04/2011] [Indexed: 11/20/2022] Open
Abstract
We report the genome organization and analysis of the first completely sequenced T4-like phage, AR1, of Escherichia coli O157:H7. Unlike most of the other sequenced phages of O157:H7, which belong to the temperate Podoviridae and Siphoviridae families, AR1 is a T4-like phage known to efficiently infect this pathogenic bacterial strain. The 167,435-bp AR1 genome is currently the largest among all the sequenced E. coli O157:H7 phages. It carries a total of 281 potential open reading frames (ORFs) and 10 putative tRNA genes. Of these, 126 predicted proteins could be classified into six viral orthologous group categories, with at least 18 proteins of the structural protein category having been detected by tandem mass spectrometry. Comparative genomic analysis of AR1 and four other completely sequenced T4-like genomes (RB32, RB69, T4, and JS98) indicated that they share a well-organized and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. The major diverse features between these phages include the modules of distal tail fibers and the types and numbers of internal proteins, tRNA genes, and mobile elements. Codon usage analysis suggested that the presence of AR1-encoded tRNAs may be relevant to the codon usage of structural proteins. Furthermore, protein sequence analysis of AR1 gp37, a potential receptor binding protein, indicated that eight residues in the C terminus are unique to O157:H7 T4-like phages AR1 and PP01. These residues are known to be located in the T4 receptor recognition domain, and they may contribute to specificity for adsorption to the O157:H7 strain.
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Affiliation(s)
- Wei-Chao Liao
- Department of Biotechnology and Laboratory Science in Medicine
| | | | | | - Wan-Jr Syu
- Institute of Microbiology and Immunology
| | - Tze-Tze Liu
- Genome Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Chuan-Hsiung Chang
- Center for Systems and Synthetic Biology
- Institute of Biomedical Informatics
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Chu LJ, Yang H, Shih P, Kao Y, Tsai YS, Chen J, Huang G, Weng RR, Ting YS, Fang X, von Haller PD, Goodlett DR, Ng WV. Metabolic capabilities and systems fluctuations in Haloarcula marismortui revealed by integrative genomics and proteomics analyses. J Proteome Res 2011; 10:3261-73. [PMID: 21598921 PMCID: PMC3168985 DOI: 10.1021/pr200290x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The 1310 Haloarcula marismortui proteins identified from mid-log and late-log phase soluble and membrane proteomes were analyzed in metabolic and cellular process networks to predict the available systems and systems fluctuations upon environmental stresses. When the connected metabolic reactions with identified proteins were examined, the availability of a number of metabolic pathways and a highly connected amino acid metabolic network were revealed. Quantitative spectral count analyses suggested 300 or more proteins might have expression changes in late-log phase. Among these, integrative network analyses indicated approximately 106 were metabolic proteins that might have growth-phase dependent changes. Interestingly, a large proportion of proteins in affected biomodules had the same trend of changes in spectral counts. Disregard the magnitude of changes, we had successfully predicted and validated the expression changes of nine genes including the rimK, gltCP, rrnAC0132, and argC in lysine biosynthesis pathway which were downregulated in late-log phase. This study had not only revealed the expressed proteins but also the availability of biological systems in two growth phases, systems level changes in response to the stresses in late-log phase, cellular locations of identified proteins, and the likely regulated genes to facilitate further analyses in the postgenomic era.
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Affiliation(s)
- Lichieh Julie Chu
- Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Hanyin Yang
- Institute of Biomedical Informatics, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Peiyin Shih
- Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Yuchieh Kao
- Institute of Biomedical Informatics, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Yihsuan Shannon Tsai
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Jinzhi Chen
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Gueitang Huang
- Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Rueyhung Roc Weng
- Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Ying Sonia Ting
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Xuefeng Fang
- Systems Biology Division, Zhejiang-California Nanosystems Institute, Zhejiang University, Hangzhou 310029, People's Republic of China
| | | | - David R. Goodlett
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Wailap Victor Ng
- Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
- Institute of Biomedical Informatics, National Yang Ming University, Taipei, Taiwan, Republic of China
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
- Clinical Biotechnology Research Center, Taipei City Hospital, Taipei, Taiwan, Republic of China
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Ahrens CH, Brunner E, Qeli E, Basler K, Aebersold R. Generating and navigating proteome maps using mass spectrometry. Nat Rev Mol Cell Biol 2010; 11:789-801. [DOI: 10.1038/nrm2973] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Nero D, Krouk G, Tranchina D, Coruzzi GM. A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule". BMC SYSTEMS BIOLOGY 2009; 3:59. [PMID: 19500399 PMCID: PMC2702358 DOI: 10.1186/1752-0509-3-59] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Accepted: 06/06/2009] [Indexed: 11/24/2022]
Abstract
BACKGROUND Nitrate-induced reprogramming of the transcriptome has recently been shown to be highly context dependent. Herein, a systems biology approach was developed to identify the components and role of cross-talk between nitrate and hormone signals, likely to be involved in the conditional response of NO3- signaling. RESULTS Biclustering was used to identify a set of genes that are N-responsive across a range of Nitrogen (N)-treatment backgrounds (i.e. nitrogen treatments under different growth conditions) using a meta-dataset of 76 Affymetrix ATH1 chips from 5 different laboratories. Twenty-one biclusters were found to be N-responsive across subsets of this meta-dataset. N-bicluster 9 (126 genes) was selected for further analysis, as it was shown to be reproducibly responsive to NO3- as a signal, across a wide-variety of background conditions and datasets. N-bicluster 9 genes were then used as "seed" to identify putative cross-talk mechanisms between nitrate and hormone signaling. For this, the 126 nitrate-regulated genes in N-bicluster 9 were biclustered over a meta-dataset of 278 ATH1 chips spanning a variety of hormone treatments. This analysis divided the bicluster 9 genes into two classes: i) genes controlled by NO3- only vs. ii) genes controlled by both NO3- and hormones. The genes in the latter group showed a NO3- response that is significantly enhanced, compared to the former. In silico analysis identified two Cis-Regulatory Elements candidates (CRE) (E2F, HSE) potentially involved the interplay between NO3- and hormonal signals. CONCLUSION This systems analysis enabled us to derive a hypothesis in which hormone signals are proposed to enhance the nitrate response, providing a potential mechanistic explanation for the link between nitrate signaling and the control of plant development.
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Affiliation(s)
- Damion Nero
- Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, 10003, USA
| | - Gabriel Krouk
- Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, 10003, USA
| | - Daniel Tranchina
- Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, 10003, USA
- Courant Institute of Mathematical Sciences, New York, 251 Mercer St, New York, NY, 10012, USA
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, 10003, USA
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Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, Baliga NS. Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. J Proteome Res 2008; 7:3755-64. [PMID: 18652504 PMCID: PMC2643335 DOI: 10.1021/pr800031f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.
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Affiliation(s)
- Phu T. Van
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Amy K. Schmid
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
| | - Nichole L. King
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
| | - Amardeep Kaur
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
| | - Min Pan
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
| | - Kenia Whitehead
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
| | - Tie Koide
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
| | - Marc T. Facciotti
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
| | - Young-Ah Goo
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Eric W. Deutsch
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
| | - David J. Reiss
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
| | - Parag Mallick
- Spielberg Family Center for Applied Proteomics, Cedars-Sinai Medical Center, 8750 W Beverly Blvd, Los Angeles, CA 90048, USA
| | - Nitin S. Baliga
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
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Ng WV, Berquist BR, Coker JA, Capes M, Wu TH, DasSarma P, DasSarma S. Genome sequences of Halobacterium species. Genomics 2008; 91:548-52; author reply 553-4. [DOI: 10.1016/j.ygeno.2008.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Accepted: 04/21/2008] [Indexed: 10/22/2022]
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Genomics and functional genomics with haloarchaea. Arch Microbiol 2008; 190:197-215. [PMID: 18493745 DOI: 10.1007/s00203-008-0376-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 04/08/2008] [Accepted: 04/20/2008] [Indexed: 10/22/2022]
Abstract
The first haloarchaeal genome was published in 2000 and today five genome sequences are available. Transcriptome and proteome analyses have been established for two and three haloarchaeal species, respectively, and more than 20 studies using these functional genomic approaches have been published in the last two years. These studies gave global overviews of metabolic regulation (aerobic and anaerobic respiration, phototrophy, carbon source usage), stress response (UV, X-rays, transition metals, osmotic and temperature stress), cell cycle-dependent transcript level regulation, and transcript half-lives. The only translatome analysis available for any prokaryotic species revealed that 10 and 20% of all transcripts are translationally regulated in Haloferax volcanii and Halobacterium salinarum, respectively. Very effective methods for the construction of in frame deletion mutants have been established recently for haloarchaea and are intensively used to unravel the biological roles of genes in this group. Bioinformatic analyses include both cross-genome comparisons as well as integration of genomic data with experimental results. The first systems biology approaches have been performed that used experimental data to construct predictive models of gene expression and metabolism, respectively. In this contribution the current status of genomics, functional genomics, and molecular genetics of haloarchaea is summarized and selected examples are discussed.
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Zhou P, Wen J, Oren A, Chen M, Wu M. Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae). Genomics 2007; 90:103-9. [PMID: 17498923 DOI: 10.1016/j.ygeno.2007.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 03/10/2007] [Accepted: 03/27/2007] [Indexed: 11/22/2022]
Abstract
We have investigated the strategy of Halobacterium sp. NRC-1 and other members of the family Halobacteriaceae to survive ultraviolet (UV) irradiation, based on an integrated analysis of various genomic and proteomic features such as dinucleotide composition and distribution of tetranucleotides in the genome and amino acid composition of the proteins. The low dipyrimidine content may help Halobacterium reduce formation of photoproducts in its genome. The usage of residues susceptible to reactive oxygen species attack is reduced significantly in Halobacterium, which helps the organism to minimize protein damage. We then correlated the expression of the zim gene with the genomic structure to reexamine the importance of the putative mismatch repair pathway proposed previously. Our results showed that Halobacterium sp. NRC-1 and other haloarchaea (Haloarcula marismortui, Haloquadratum walsbyi) have optimized their genomic and proteomic structures to reduce damage induced by UV irradiation, often present at high levels in habitats where these organisms thrive.
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Affiliation(s)
- Peng Zhou
- Department of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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DasSarma S, Berquist BR, Coker JA, DasSarma P, Müller JA. Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1. SALINE SYSTEMS 2006; 2:3. [PMID: 16542428 PMCID: PMC1447603 DOI: 10.1186/1746-1448-2-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 03/16/2006] [Indexed: 11/21/2022]
Abstract
Halobacteriumsp. NRC-1 is an extremely halophilic archaeon that is easily cultured and genetically tractable. Since its genome sequence was completed in 2000, a combination of genetic, transcriptomic, proteomic, and bioinformatic approaches have provided insights into both its extremophilic lifestyle as well as fundamental cellular processes common to all life forms. Here, we review post-genomic research on this archaeon, including investigations of DNA replication and repair systems, phototrophic, anaerobic, and other physiological capabilities, acidity of the proteome for function at high salinity, and role of lateral gene transfer in its evolution.
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Affiliation(s)
- Shiladitya DasSarma
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - Brian R Berquist
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - James A Coker
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - Priya DasSarma
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - Jochen A Müller
- Department of Biology, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD 21251, USA
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