Mini review of Methanothermococcus okinawensis genome

Мне ужасно стыдно за этот обзор, по-хорошему его надо переделывать и сильно.

Abstract

Methanothermococcus okinawensis is a thermophilic methane-producing archaeon. In this review there is an attempt to retrieve and analyze some information from its genome such as nucleotide composition, statistical data about its proteome and ribosomal genes.

  1. Introduction

    2. Methanothermococcus okinawensis is a thermophilic, methaneproducing archaeon first isolated from a deep-sea hydrothermal vent chimney at the Iheya Ridge, in the Okinawa Trough, Japan, in 2000. It appeared to be strictly an anaerobic, mesophilic autotroph that uses hydrogen as a source of electrons, carbon dioxide or formate as a source of carbon and electron acceptor and ammonium as a nitrogen source.[1]

    Such organisms with unique biochemical pathways are important in fundamental research, including the ones about extraterrestrial life, [2] and can be applied in biotechnology.[3]

    Methanothermococcus okinawensis electron micrograph
    Fig. 1. Electron micrograph of negatively stained cells. The polar bundle of flagella is observed. Bar, 400 nm (Ken Takai et al. 2002)

  2. Methods

    3. Python programming: Google Colab notebook with python codes used here.

    Excel: table with histogram showing distribution of proteins by length.

  3. Results

    1. Standard data about Metanothermococcus okinawensis genome

      2. Metanothermococcus okinawensis has 2 DNA sequences: a chromosome and a plasmid pMETOK01. Frequencies of nucleotides were counted and are shown in Table 1. According to them one can see that Chargaff’s rules work but are more accurate for longer sequences.

      Table 1. Frequencies of nucleotides and GC content in M. okinawensis chromosome and in plasmid pMETOK01
      Sequence name Sequence length, bp Nucleotide frequencies GC content
      A T G C
      Methanothermococcus okinawensis IH1, complete sequence 1662525 0.35321 0.35380 0.14595 0.14703 0.29299
      Methanothermococcus okinawensis IH1 plasmid pMETOK01, complete sequence 14930 0.39699 0.33463 0.14856 0.11983 0.26839

      Also, frequencies of nucleotides and GC content were counted separately for CDS and not CDS – see Table 2. GC content is much higher in CDS, but still less than 0.5, which would be expected if nucleotides appeared randomly with equal probability 0.25. One of the reasons is different probability of mutations from one nucleotide to another. Quite often occurs such mutation as methylcytosine deamination that results in forming thymine. Cytosine can be modified in CpG dinucleotides including methylation and this mutation is difficult for DNA repair systems.[4] As a result, frequencies of cytosine and guanine are lower than those of adenine and thymine and GC content is less than 0.5. However, in CDS stabilizing selection is more present than in not CDS, so GC content is higher in CDS.

      Table 2. Frequencies of nucleotides and GC content in and out of CDS
      Sequence name CDS/not CDS Nucleotide frequencies GC content
      A T G C
      Methanothermococcus okinawensis IH1, complete sequence CDS 0.34268 0.34416 0.15585 0.15731 0.31316
      Not CDS 0.40748 0.40349 0.09494 0.09409 0.18903
      Methanothermococcus okinawensis IH1 plasmid pMETOK01, complete sequence CDS 0.38823 0.33424 0.15203 0.12550 0.27753
      Not CDS 0.35295 0.35395 0.14591 0.14719 0.29310

    2. Statistical data about M. okinawensis proteome

      1. Distribution of proteins by length

        2. As can be seen from Fig. 2 most of proteins have length between 50 and 450 amino acid residues.

        Fig. 2. Distribution of proteins by length
      2. Number of genes, coded on direct and complementary DNA chains

        3. The null hypothesis (H0) is that genes are randomly distributed between direct and complementary chains with equal probabilities. Chi square equals 0.1402 with p-value 0.7081 that is much more than 0.05, so it is very likely that the null hypothesis is correct.

        Table 3. Number of genes coded on direct (+) and complementary (-) DNA chains of M. okinawensis
        Sequence name + -
        Methanothermococcus okinawensis IH1, complete sequence 795 810
        Methanothermococcus okinawensis IH1 plasmid pMETOK01, complete sequence 4 6

        Genes are approximately evenly distributed between + and – DNA chains.

      3. Number of ribosomal, hypothetical and transport proteins

        4. Ribosomal, hypothetical and transport proteins were counted distinctly for Methanothermococcus okinawensis chromosome and plasmid

        Table 4. Number of different types of proteins in Methanothermococcus okinawensis proteome
        Type of proteins Number of proteins Proportion of proteins in total number of proteins
        Ribosomal proteins M. okinawensis IH1 chromosome 63 0.0383
        IH1 plasmid pMETOK01 0 0.0
        Hypothetical proteins M. okinawensis IH1 chromosome 276 0.1680
        IH1 plasmid pMETOK01 6 0.5455
        Transport proteins M. okinawensis IH1 chromosome 67 0.0408
        IH1 plasmid pMETOK01 0 0.0

    3. Statistical data about ribosomal genes

      4. The number of RNA coding genes is much lower than the number of protein coding genes. Except for tRNA coding genes there are two other non-coding RNA (ncRNA) genes: ribonuclease P (RNase P) – a ribozyme that cleaves tRNA precursor molecules,[5] and SRP RNA that recognizes signal peptide of membrane or secretory proteins and then associates with SRP receptor anchored to endoplasmic reticulum membrane.[6]

      Table 5. Number of RNA coding genes in M. okinawensis compared to the number of protein coding genes
      Type of gene product Number of genes
      Protein coding genes 1615
      All RNA coding genes 47
      rRNA coding genes 7
      tRNA coding genes 38

    4. Cumulative GC skew

      5. Cumulative GC skew for the chromosome and for the plasmid are shown in Fig. 3 and Fig. 4 respectively. Minimum in cumulative GC skew for the plasmid corresponds with minimum in GC content that is shown in Fig. 5. Peaks on this graph must be referring to genes, while the lowest GC content probably marks origin of replication.

      Methanothermococcus okinawensis chromosome cumulstive GC skew
      Fig. 3. Cumulative GC skew in Methanothermococcus okinawensis chromosome
      Window length – 100000 nucleotides, step – 1000 nucleotides. Minimal value is -13.92554, in coordinate 1524000, maximal value is 9.09971, in coordinate 305000
      Methanothermococcus okinawensis plasmid cumulative GC skew
      Fig. 4. Cumulative GC skew in Methanothermococcus okinawensis plasmid pMETOK01
      Window length – 500 nucleotides, step – 50 nucleotides. Minimal value is -5.46870, in coordinate 2600, maximal value is 42.52213, in coordinate 12350
      Methanothermococcus okinawensis plasmid GC content
      Fig. 5. GC content in Methanothermococcus okinawensis plasmid pMETOK01
      Window length – 500 nucleotides, step – 50 nucleotides. Minimal value is - 0.164, in coordinate 1600, maximal value is 0.36, in coordinate 1050

References

  1. Ken Takai et al. (2002) Methanothermococcus okinawensis sp. nov., a thermophilic, methane-producing archaeon isolated from a Western Pacific deep-sea hydrothermal vent system doi: 10.1099/ijs.0.02106-0
  2. Ruth-Sophie Taubner et al. (2018) Biological methane production under putative Enceladus-like conditions doi: 10.1038/s41467-018-02876-y
  3. Lisa-Maria Mauerhofer et al. (2021) Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories doi: 10.1038/s42003-021-01828-5
  4. Akira Sassa et al. (2016) M. Mutagenic consequences of cytosine alterations site-specifically embedded in the human genome doi: 10.1186/s41021-016-0045-9
  5. CeciliaGuerrier-Takada et al. (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme doi: 10.1016/0092-8674(83)90117-4
  6. Kiyoshi Nagai (2003) Structure, function and evolution of the signal recognition particle https://doi.org/10.1093/emboj/cdg337