Friedhelm Pfeiffer

• PhD
• Senior Researcher at Max Planck Institute of Biochemistry

Haloferax volcanii harbours four putative proviruses: Halfvol1, Halfvol2, Halfvol3 and Halfvol4. In this study we successfully deleted all four provirus genomes, demonstrating, that they are not essential. Transcriptome comparison between this strain (ΔHalfvol1-4) and a wild type strain reveals an increase in archaella and chemotaxis gene expressio...

A consortium of landfill bacteria including strain G3 can break down polyethylene, a long-lasting plastic that accumulates in the environment. The complete genome sequence of strain G3 was determined by PacBio and Nanopore sequencing and consists of three circular replicons. Genome-based classification assigned strain G3 to the species Pseudomonas...

Lipoproteins are major constituents of prokaryotic cell surfaces. In bacteria, lipoprotein attachment to membrane lipids is catalyzed by prolipoprotein diacylglyceryl transferase (Lgt). However, no Lgt homologs have been identified in archaea, suggesting the unique archaeal membrane lipids require distinct enzymes for lipoprotein lipidation. Here,...

The response of the haloarchaeal model organism Haloferax volcanii to iron starvation was analyzed at the proteome level by data-independent acquisition mass spectrometry. Cells grown in minimal medium with normal iron levels were compared to those grown under low iron conditions, with samples being separated into membrane and cytoplasmic fractions...

Eight colonies of live microbes were isolated from an extensively surface-sterilized halite sample which had been retrieved from a depth of 2000 m from a salt mine in the Qianjiang Depression, Hubei Province, PR China. The eight colonies, obtained after 4 weeks of incubation, were named JI20-1 T –JI20-8 and JI20-1 T was selected as the type strain....

Archaea play indispensable roles in global biogeochemical cycles, yet many crucial cellular processes, including cell-shape determination, are poorly understood. Haloferax volcanii, a model haloarchaeon, forms rods and disks, depending on growth conditions. Here, we used a combination of iterative proteomics, genetics, and live-cell imaging to iden...

Genomes of bacteria and archaea contain a much larger fraction of unidirectional (serial) gene pairs than convergent or divergent gene pairs. Many of the unidirectional gene pairs have short overlaps of −4 nt and −1 nt. As shown previously, translation of the genes in overlapping unidirectional gene pairs is tightly coupled. Two alternative models...

Archaea play indispensable roles in global biogeochemical cycles, yet many critical cellular processes, including cell-shape determination, are poorly understood. Haloferax volcanii , a model haloarchaeon, forms rods and disks, depending on growth conditions. Here, we used a combination of iterative proteomics, genetics, and live-cell imaging to id...

Nine different bacterial isolates were recovered from landfills. Each isolate was obtained in pure culture. As a consortium, the bacteria degrade polyethylene. The complete genome sequence of strain G5 was determined by PacBio sequencing. Using the TYGS for taxonomic classification, strain G5 was assigned to the species Cupriavidus campinensis.

Nine different bacterial isolates were recovered from landfills. Each isolate was obtained in pure culture. As a consortium, the bacteria degrade polyethylene. The complete genome sequence of strain G2 was determined by PacBio sequencing. Using the TYGS for taxonomic classification, strain G2 was assigned to the species Pseudomonas veronii .

Nine different bacterial isolates were recovered from landfills. Each isolate was obtained in pure culture. As a consortium, the bacteria degrade polyethylene. The complete genome sequence of strain G9 was determined by PacBio sequencing. Using the TYGS server for taxonomic classification, strain G9 was assigned to the species Micromonospora aurant...

The halophilic γ-proteobacterium Halomonas elongata DSM 2581 T thrives at salt concentrations well above 10 % NaCl (1.7 M NaCl). A well-known osmoregulatory mechanism is the accumulation of the compatible solute ectoine within the cell in response to osmotic stress. While ectoine accumulation is central to osmoregulation and promotes resistance to...

Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both classes of repeat contain AT-rich motifs that were conjectured to represent promoters. In the present...

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 annotat...

Glycosylation is one of the most complex posttranslational protein modifications. Its importance has been established not only for eukaryotes but also for a variety of prokaryotic cellular processes, such as biofilm formation, motility, and mating. However, comprehensive glycoproteomic analyses are largely missing in prokaryotes. Here, we extend th...

Hardyhisp2 virus infects the halophilic archaeon Haloarcula hispanica DSM 4426 T and is closely related to His2 ( Pleolipoviridae family). The viral genome is 16,133 bp long, with terminal inverted repeats of 599 bp. The predicted spike protein is only weakly similar (32% amino acid identity) to that of His2.

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 annotat...

Hypersaline environments are the source of many viruses infecting different species of halophilic euryarchaea. Information on infection mechanisms of archaeal viruses is scarce, due to the lack of genetically accessible virus–host models. Recently, a new archaeal siphovirus, Haloferax tailed virus 1 (HFTV1), was isolated together with its host belo...

The virus Hardycor1 was isolated in 1998 and infects the haloarchaeon Halorubrum coriense. DNA from a frozen stock (HC1) was sequenced and the viral genome found to be 45,142 bp of dsDNA, probably having redundant, circularly permuted termini. The genome showed little similarity (BLASTn) to known viruses. Only twenty-two of the 53 (41%) predicted p...

Glycosylation is one of the most complex post-translational protein modifications. Its importance has been established not only for eukaryotes but also for a variety of prokaryotic cellular processes, such as biofilm formation, motility and mating. However, comprehensive glycoproteomic analyses are largely missing in prokaryotes. Here we extend the...

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_2...

Hypersaline environments are the source of many viruses infecting different species of halophilic euryarchaea. Information on infection mechanisms of archaeal viruses is scarce, due to the lack of genetically accessible virus-host models. Recently a new archaeal siphovirus, Haloferax tailed virus 1 (HFTV1), was isolated together with its host belon...

While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific b...

For osmoadaptation the halophilic bacterium Halomonas elongata synthesizes as its main compatible solute the aspartate derivative ectoine. H. elongata does not rely entirely on synthesis but can accumulate ectoine by uptake from the surrounding environment with the help of the osmoregulated transporter TeaABC. Disruption of the TeaABC-mediated ecto...

Few genomes of the HF1-group of viruses are currently available, and further examples would enhance the understanding of their evolution, improve their gene annotation, and assist in understanding gene function and regulation. Two novel HF1-group haloviruses, Serpecor1 and Hardycor2, were recovered from widely separated hypersaline lakes in Austral...

The subcellular organization of biochemical processes in space and time is still one of the most mysterious topics in archaeal cell biology. Despite the fact that haloarchaea largely rely on covalent lipid anchoring to coat the cell envelope, little is known about how cells coordinate de novo synthesis and about the insertion of this proteinaceous...

Archaeal genomes are densely packed; thus, correct transcription termination is an important factor for orchestrated gene expression. A systematic analysis of RNA 3´ termini, to identify transcription termination sites (TTS) using RNAseq data has hitherto only been performed in two archaea, Methanosarcina mazei and Sulfolobus acidocaldarius. In thi...

The archaeal cytoplasmic membrane provides an anchor for many surface proteins. Recently, a novel membrane anchoring mechanism involving a peptidase, archaeosortase A (ArtA) and C-terminal lipid attachment of surface proteins was identified in the model archaeon Haloferax volcanii. ArtA is re-quired for optimal cell growth and morphogenesis, and th...

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 betw...

In haloarchaea, a cluster of three genes is localized directly adjacent to the major replication origin, and, hence, the encoded proteins were annotated as 'origin-associated proteins' (Oap). However, prior to this study, no experimental data were available for these conserved hypothetical proteins. Bioinformatics analyses were performed, which unr...

We performed an in‐depth proteome analysis of the haloarchaeal model organism Haloferax volcanii under standard, low/high salt and low/high temperature conditions using label‐free mass spectrometry. Qualitative analysis of protein identification data from high‐pH/reversed phase fractionated samples indicated 61.1% proteome coverage (2,509 proteins)...

Archaea are motile by the rotation of the archaellum. The archaellum switches between clockwise and counterclockwise rotation, and movement along a chemical gradient is possible by modulation of the switching frequency. This modulation involves the response regulator CheY and the archaellum adaptor protein CheF. In this study, two new crystal forms...

Archaeal genomes are densely packed; thus, correct transcription termination is an important factor for orchestrated gene expression. A systematic analysis of RNA 3’ termini, to identify transcription termination sites (TTS) using RNAseq data has hitherto only been performed in two archaea. In this study, only part of the genome had been investigat...

High-coverage long-read sequencing of the Halobacterium salinarum type strain (91-R6) revealed a 2.17-Mb chromosome and two large plasmids (148 and 102 kb). Population heterogeneity and long repeats were observed. Strain 91-R6 and laboratory strain R1 showed 99.63% sequence identity in common chromosomal regions and only 38 strain-specific segments...

Haloferax volcanii is a well-established model species for haloarchaea. Small scale RNomics and bioinformatics predictions were used to identify small non-coding RNAs (sRNAs), and deletion mutants revealed that sRNAs have important regulatory functions. A recent dRNA-Seq study was used to characterize the primary transcriptome. Unexpectedly, it was...

Comparison of three codon usage tables: 1) the codon usage table computed from the more than 4000 protein coding genes of H. volcanii, 2) the codon usage table computed from the 1077 small proteins of up to 150 amino acids from H. volcanii, and 3) the codon usage table for E. coli. (DOC)

Oligonucleotides that were used to generate probes for the Northern blot analyses. (DOC)

Detection of an upstream sRNA (rather than a very long 5’-UTR). A. Screenshot from the Integrated Genome Browser. For explanations of panels see Fig 2. B. Northern blot analysis. (PPTX)

Example for one gene that is transcribed into two transcript isoforms of different lengths and example for overlapping 3’-ends of RNAs. A. Screenshot from the Integrated Genome Browser. For explanations of panels see Fig 2. B. Northern blot analysis with probe a. C. Northern blot analysis with probe b. (PPTX)

Example for two isoforms of an asRNA. A. Screenshot from the Integrated Genome Browser. For explanations of panels see Fig 1. B. Northern blot analysis with probe a. C. Northern blot analysis with probe b. (PPTX)

Complete uncropped versions of all Northern blots shown in the Figs 1 and 5–7, and S2–S6. (PPTX)

Results of previous RNA-Seq and dRNA-Seq studies with archaea. (DOC)

Summary of results of the RNA-Seq study. The Table lists the predicted RNAs, their genomic locations and their lengths. It also includes the associated HVO_number (gene identifier), presence of overlapping 3’-UTRs, and number of genes on polycistronic transcripts. For cdRNAs, the identification in the previous dRNA-Seq study is flagged [19]. (XLSX)

Examples of RNA-Seq results and the comparison with the genome annotation and dRNA-Seq results. Screenshots from the Integrated Genome Browser are shown. The upper half shows results from the top strand, the lower half from the bottom strand. The middle line represents the genome sequence, genome positions are indicated. The following data are show...

Detection of a very long 5’-UTR (rather than an upstream sRNA). A. Screenshot from the Integrated Genome Browser. For explanations of panels see Fig 2. B. Northern blot analysis. (PPTX)

Detection of a very long 3’-UTR. A. Screenshot from the Integrated Genome Browser. For explanations of panels see Fig 2. B. Northern blot analysis. (PPTX)

The unexpected lysis of a large culture of Halobacterium salinarum strain S9 was found to be caused by a novel myovirus, designated ChaoS9. Virus purification from the culture lysate revealed a homogeneous population of caudovirus-like particles. The viral genome is linear, dsDNA that is partially redundant and circularly permuted, has a unit lengt...

Background Photorhabdus luminescens is an enteric bacterium, which lives in mutualistic association with soil nematodes and is highly pathogenic for a broad spectrum of insects. A complete genome sequence for the type strain P. luminescens subsp. laumondii TT01, which was originally isolated in Trinidad and Tobago, has been described earlier. Subse...

Microorganisms can move towards favorable growth conditions as a response to environmental stimuli. This process requires a motility structure and a system to direct the movement. For swimming motility, archaea employ a rotating filament, the archaellum. This archaea-specific structure is functionally equivalent, but structurally different, from th...

The halophilic myohalovirus Halobacterium virus phiH (ΦH) was first described in 1982 and was isolated from a spontaneously lysed culture of Halobacterium salinarum strain R1. Until 1994, it was used extensively as a model to study the molecular genetics of haloarchaea, but only parts of the viral genome were sequenced during this period. Using San...

Cell surfaces are critical for diverse functions across all domains of life, from cell-cell communication and nutrient uptake to cell stability and surface attachment. While certain aspects of the mechanisms supporting the biosynthesis of the archaeal cell surface are unique, likely due to important differences in cell surface compositions between...

Plasmids PL6A and PL6B are both carried by the C23T strain of the square archaeon Haloquadratum walsbyi, and are closely related (76% nucleotide identity), circular, about 6 kb in size, and display the same gene synteny. They are unrelated to other known plasmids and all of the predicted proteins are cryptic in function. Here we describe two additi...

Background: Protein or nucleic acid sequences contain a multitude of associated annotations representing continuous sequence elements (CSEs). Comparing these CSEs is needed, whenever we want to match identical annotations or integrate distinctive ones. Currently, there is no ready-to-use software available that provides comprehensive statistical r...

Background Due to the predominant usage of short-read sequencing to date, most bacterial genome sequences reported in the last years remain at the draft level. This precludes certain types of analyses, such as the in-depth analysis of genome plasticity. ResultsHere we report the finalized genome sequence of the environmental strain Aeromonas salmon...

The genome of the Halomonas elongata type strain DSM 2581, an industrial producer, was reevaluated using the Illumina HiSeq2500 technology. To resolve duplication-associated ambiguities, PCR products were generated and sequenced. Outside of duplications, 72 sequence corrections were required, of which 24 were point mutations and 48 were indels of o...

Importance: Thiamine pyrophosphate (TPP) is a cofactor needed for the enzymatic activity of many cellular processes including central metabolism. In archaea, thiamine biosynthesis is an apparent chimera of eukaryotic- and bacterial-type pathways that is not well defined at the level of enzymatic steps or regulatory mechanisms. Here we find ThiN to...

Halophilic bacteria use a variety of osmoregulatory methods, such as the accumulation of one or more compatible solutes. The wide diversity of compounds that can act as compatible solute complicates the task of understanding the different strategies that halophilic bacteria use to cope with salt. This is specially challenging when attempting to go...

Supporting Information PCR. Figures A to W and Table A. (DOCX)

Supporting Information Model. Table D. (XLSX)

Supporting Information Proteome. Tables B and C. (DOCX)

Background Differential RNA-Seq (dRNA-Seq) is a recently developed method of performing primary transcriptome analyses that allows for the genome-wide mapping of transcriptional start sites (TSSs) and the identification of novel transcripts. Although the transcriptomes of diverse bacterial species have been characterized by dRNA-Seq, the transcript...

The archaeon Halobacterium salinarum can produce energy using three different processes, namely photosynthesis, oxidative phosphorylation and fermentation of arginine, and is thus a model organism in bioenergetics. Compared to its bacteriorhodopsin-driven photosynthesis, less attention has been devoted to modeling its respiratory pathway. We create...

Supplementary Text and Figures. The supplementary text contains details about the derivation of cellular constants, medium constants and initial conditions. The file also contains parameter sensitivity results and model output using all parameter sets. (PDF)

Matlab code for parameter estimation and for plotting results. We provide a set of scripts that can be used to plot the model output using the parameter sets in Tables 2 and 3. An example of parameter estimation to obtain parameter set EN3 is provided. Also provided are scripts that can be used for converting experimental measurements into differen...

Live microbes have been isolated from rock salt up to Permian age. Only obligatory cellular functions can be performed in halite-buried cells. Consequently, their genomic sequences are likely to remain virtually unchanged. However, the available sequence information from these organisms is scarce, and consists of mainly ribosomal 16S sequences. Her...

Genome annotation errors are a persistent problem that impede research in the biosciences. A manual curation effort is described that attempts to produce high-quality genome annotations for a set of haloarchaeal genomes (Halobacterium salinarum and Hbt. hubeiense, Haloferax volcanii and Hfx. mediterranei, Natronomonas pharaonis and Nmn. moolapensis...

At the time of its first publication, halomucin from Haloquadratum walsbyi strain HBSQ001 was the largest archaeal protein known (9159 aa). It has a predicted signal sequence, making it likely to be an extracellular or secreted protein. Best BLAST matches were found to be mammalian mucins that protect tissues to dehydration and chemical stress. It...

Background Thiamine (vitamin B1) is synthesized de novo by certain yeast, fungi, plants, protozoans, bacteria and archaea. The pathway of thiamine biosynthesis by archaea is poorly understood, particularly the route of sulfur relay to form the thiazole ring. Archaea harbor structural homologs of both the bacterial (ThiS-ThiF) and eukaryotic (THI4)...

It was long assumed that translation initiation in prokaryotes generally occurs via the so-called Shine Dalgarno (SD) mechanism. Recently, it became clear that translation initiation in prokaryotes is more heterogeneous. In the haloarchaeon Haloferax volcanii, the majority of transcripts is leaderless and most transcripts with a 5'-UTR lack a SD mo...

Cell surfaces are decorated by a variety of proteins that facilitate interactions with their environments and support cell stability. These secreted proteins are anchored to the cell by mechanisms that are diverse, and, in archaea, poorly understood. Recently published in silico data suggest that in some species a subset of secreted euryarchaeal pr...

The genus Natronomonas contains two species, one haloalkaliphile (N. pharaonis) and one neutrophile (N. moolapensis). Here, we report the genome sequence of N. moolapensis strain 8.8.11. The overall genome properties are similar for the two species. Only the neutrophile contains bacteriorhodopsin and a membrane glycolipid.

Prokaryotes have developed several strategies to defend themselves against foreign genetic elements. One of those defense mechanisms is the recently identified CRISPR/Cas system, which is used by approximately half of all bacterial and almost all archaeal organisms. The CRISPR/Cas system differs from the other defense strategies because it is adapt...

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system provides adaptive and heritable immunity against foreign genetic elements in most archaea and many bacteria. Although this system is widespread and diverse with many subtypes, only a few species have been investigated to elucidate the precise mechan...

Salt acclimation in moderately halophilic bacteria is the result of action of a grand interplay orchestrated by signals perceived from the environment. To elucidate the cellular players involved in sensing and responding to changing salinities we have determined the genome sequence of Halobacillus halophilus, a Gram-positive moderate halophilic bac...

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...

Table S1.Natrialba magadii ATCC 43099 genes discussed in the text. This table lists Nab. magadii ATCC 43099 genes related to bacteriophage and recombination elements, rRNA genes, and genes encoding adaptive features.

Table S4. Natrialba magadii ATCC 43099 genes involved in metabolism. This table lists Nab. magadii ATCC 43099 genes encoding molybdenum cofactor biosynthesis and other metabolic functions.

Table S2. Bidirectional best blast pairs among proteins fromNatrialba magadii and 17 other haloarchaeal genomes. This table lists the number of bidirectional best blast pairs among proteins from Nab. magadii and 17 other halophilic archaea. The first column is the number of total proteins in each genome, the second column is the number of bidirecti...

Table S3.Natrialba magadii ATCC 43099 genes encoding putative peptidases/proteases, protease inhibitors, and regulatory proteins. This table lists Nab. magadii ATCC 43099 genes encoding various types of proteases and peptidases as well as protease inhibitors and regulatory proteins.

Accession numbers of all replicons in this genome project: HE717023, HE717024, HE717025.

Accession numbers for all replicons in this genome project: HE717023, HE717024, HE717025.